3MPR

Crystal Structure of endonuclease/exonuclease/phosphatase family protein from Bacteroides thetaiotaomicron, Northeast Structural Genomics Consortium Target BtR318A

PDB DOI: https://doi.org/10.2210/pdb3MPR/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-27 Released: 2010-05-26
Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.204 (Depositor), 0.200 (DCC)
R-Value Work:
0.156 (Depositor), 0.153 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target BtR318A

Kuzin, A., Su, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

To be published.

Macromolecule Content

Total Structure Weight: 140.08 kDa
Atom Count: 10,382
Modelled Residue Count: 1,109
Deposited Residue Count: 1,192
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative endonuclease/exonuclease/phosphatase family protein	A, B, C, D	298	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_3783
UniProt
Find proteins for Q8A183 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A183 Go to UniProtKB: Q8A183
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A183
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C]	BA [auth C], CA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Y [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain W [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth C]	AA [auth C] FA [auth D] G [auth A] GA [auth D] H [auth A] AA [auth C], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], K [auth A], U [auth B], V [auth B], W [auth B], Y [auth C], Z [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain T [auth B] SDF format, chain DA [auth D] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain T [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain X [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain T [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain X [auth C]	DA [auth D] E [auth A] EA [auth D] F [auth A] T [auth B] DA [auth D], E [auth A], EA [auth D], F [auth A], T [auth B], X [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain T [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain T [auth B] Focus chain X [auth C]
UNL Query on UNL Download Ideal Coordinates CCD File	L [auth A] M [auth A] N [auth A] O [auth A] P [auth A] L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	Unknown ligand QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.204 (Depositor), 0.200 (DCC)
R-Value Work: 0.156 (Depositor), 0.153 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.643	α = 90
b = 103.143	β = 103.39
c = 79.811	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary