4K8G | pdb_00004k8g

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 (Depositor), 0.148 (DCC)
R-Value Work:
0.141 (Depositor), 0.141 (DCC)
R-Value Observed:
0.141 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4K8G

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
Modeled Residue Count: 386
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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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 EC: 4.2.1.8
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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] mmCIF 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 (Depositor), 0.148 (DCC)
R-Value Work: 0.141 (Depositor), 0.141 (DCC)
R-Value Observed: 0.141 (Depositor)

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

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View more in-depth experimental data

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.