5F4Z | pdb_00005f4z

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

PDB DOI: https://doi.org/10.2210/pdb5F4Z/pdb

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

Deposited: 2015-12-03 Released: 2016-02-17
Deposition Author(s): Tan, K., Li, H., Jedrzejczak, R., BABNIGG, G., BINGMAN, C.A., YENNAMALLI, R., LOHMAN, J., Chang, C.Y., Shen, B., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.160 (Depositor), 0.160 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

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

Tan, K., Li, H., Jedrzejczak, R., BABNIGG, G., BINGMAN, C.A., YENNAMALLI, R., LOHMAN, J., Chang, C.Y., Shen, B., Phillips Jr., G.N., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 220.82 kDa
Atom Count: 16,650
Modeled Residue Count: 1,944
Deposited Residue Count: 1,965
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase	A, B, C, D, E	393	Streptomyces carzinostaticus subsp. neocarzinostaticus	Mutation(s): 0
UniProt
Find proteins for Q84HB1 (Streptomyces carzinostaticus subsp. neocarzinostaticus) Explore Q84HB1 Go to UniProtKB: Q84HB1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q84HB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
5V4 Query on 5V4 Download Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain M [auth A] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A]	M [auth A], Q [auth B], S [auth C], T [auth D], V [auth E]	(1~{R},2~{R})-2,3-dihydro-1~{H}-indene-1,2-diol C₉ H₁₀ O₂ YKXXBEOXRPZVCC-RKDXNWHRSA-N		Interactions Focus chain M [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain V [auth E] Interactions & Density Focus chain M [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain V [auth E]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain U [auth E] SDF format, chain R [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain U [auth E] MOL2 format, chain R [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain U [auth E] mmCIF format, chain R [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], R [auth C], U [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions 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 R [auth C] Focus chain U [auth E] Interactions & Density 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 R [auth C] Focus chain U [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A]	K [auth A], N [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain K [auth A] Focus chain N [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.160 (Depositor), 0.160 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.356	α = 90
b = 93.068	β = 115.33
c = 134.059	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History (Full details and data files)

Version 1.0: 2016-02-17
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-02-06
Changes: Data collection, Source and taxonomy
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 1.4: 2020-09-23
Changes: Database references, Structure summary
Version 1.5: 2024-11-06
Changes: Data collection, Database references, Structure summary