4K8G

Crystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans mutant (V161A, R163A, K165G, L166A, Y167G, Y168A, E169G)

PDB DOI: https://doi.org/10.2210/pdb4K8G/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-04-18 Released: 2013-05-22
Deposition Author(s): Lukk, T., Wichelecki, D., Gerlt, J.A., Nair, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.148
R-Value Work: 0.141
R-Value Observed: 0.141

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans mutant (V161A, R163A, K165G, L166A, Y167G, Y168A, E169G)

Wichelecki, D., Lukk, T., Nair, S.K., Gerlt, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 47.09 kDa
Atom Count: 3,721
Modelled Residue Count: 386
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein	A	422	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 7 Gene Names: Saro_3675
UniProt
Find proteins for A4XF23 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XF23 Go to UniProtKB: A4XF23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4XF23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.148
R-Value Work: 0.141
R-Value Observed: 0.141
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.77	α = 90
b = 125.77	β = 90
c = 119.74	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-22
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.