3BWX

Crystal structure of an alpha/beta hydrolase (YP_496220.1) from Novosphingobium aromaticivorans DSM 12444 at 1.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BWX/pdb

Classification: HYDROLASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-01-10 Released: 2008-01-22
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.203
R-Value Work: 0.161
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of an alpha/beta hydrolase (YP_496220.1) from Novosphingobium aromaticivorans DSM 12444 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 33.05 kDa
Atom Count: 2,604
Modelled Residue Count: 285
Deposited Residue Count: 285
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase	A	285	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 1 Gene Names: YP_496220.1, Saro_0941
UniProt
Find proteins for Q2G9T7 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2G9T7 Go to UniProtKB: Q2G9T7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G9T7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [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], K [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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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 K [auth A] 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 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] 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]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [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: 1.50 Å
R-Value Free: 0.203
R-Value Work: 0.161
R-Value Observed: 0.163
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33BWX

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.48	α = 90
b = 69.95	β = 90
c = 82.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-01-22

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-01-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-01-25
Changes: Database references
Version 1.6: 2024-11-13
Changes: Data collection, Structure summary