4I19

The crystal structure of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus.

PDB DOI: https://doi.org/10.2210/pdb4I19/pdb

Classification: HYDROLASE
Organism(s): Streptomyces carzinostaticus subsp. neocarzinostaticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-11-20 Released: 2012-12-05
Deposition Author(s): Tan, K., Bigelow, L., Clancy, S., Babnigg, G., Bingman, C.A., Yennamalli, R., Lohman, J., Ma, M., Shen, B., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.209 (Depositor), 0.206 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus.

Tan, K., Bigelow, L., Clancy, S., Babnigg, G., Bingman, C.A., Yennamalli, R., Lohman, J., Ma, M., Shen, B., Phillips Jr., G.N., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 44.32 kDa
Atom Count: 3,259
Modelled Residue Count: 386
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase	A	388	Streptomyces carzinostaticus subsp. neocarzinostaticus	Mutation(s): 0
UniProt
Find proteins for Q84HB8 (Streptomyces carzinostaticus subsp. neocarzinostaticus) Explore Q84HB8 Go to UniProtKB: Q84HB8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q84HB8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
FMT Query on FMT 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 H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] 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 H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] 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 H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.209 (Depositor), 0.206 (DCC)
R-Value Work: 0.162 (Depositor), 0.162 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.011	α = 90
b = 76.011	β = 90
c = 161.263	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History (Full details and data files)

Version 1.0: 2012-12-05
Type: Initial release
Version 1.1: 2013-01-30
Changes: Structure summary
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary