4JDP | pdb_00004jdp

Crystal structure of probable p-nitrophenyl phosphatase (pho2) (target EFI-501307) from Archaeoglobus fulgidus DSM 4304 with Magnesium bound

PDB DOI: https://doi.org/10.2210/pdb4JDP/pdb

Classification: HYDROLASE
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-02-25 Released: 2013-03-06
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Allen, K.N., Dunaway-Mariano, D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.206 (Depositor), 0.211 (DCC)
R-Value Work:
0.170 (Depositor), 0.182 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of probable p-nitrophenyl phosphatase from Archaeoglobus fulgidus.

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N.F., Stead, M., Love, J., Allen, K.N., Dunaway-Mariano, D., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 63.68 kDa
Atom Count: 4,623
Modeled Residue Count: 529
Deposited Residue Count: 574
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
p-nitrophenyl phosphatase (Pho2)	A, B	287	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: AF_0374
UniProt
Find proteins for O29873 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29873 Go to UniProtKB: O29873
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29873
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.206 (Depositor), 0.211 (DCC)
R-Value Work: 0.170 (Depositor), 0.182 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.559	α = 90
b = 64.733	β = 90
c = 135.062	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description