4WJI | pdb_00004wji

Crystal structure of cyclohexadienyl dehydrogenase from Sinorhizobium meliloti in complex with NADP and tyrosine

PDB DOI: https://doi.org/10.2210/pdb4WJI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-09-30 Released: 2014-10-22
Deposition Author(s): Shabalin, I.G., Cooper, D.R., Hou, J., Zimmerman, M.D., Stead, M., Hillerich, B.S., Ahmed, M., Hammonds, J., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.159 (Depositor), 0.158 (DCC)
R-Value Work:
0.115 (Depositor), 0.115 (DCC)
R-Value Observed:
0.117 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of cyclohexadienyl dehydrogenase from Sinorhizobium meliloti in complex with NADP

Shabalin, I.G., Cooper, D.R., Hou, J., Zimmerman, M.D., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 32.74 kDa
Atom Count: 2,522
Modeled Residue Count: 293
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase	A	293	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: tyrC EC: 1.3.1 (PDB Primary Data), 1.3.1.12 (UniProt)
UniProt
Find proteins for Q92MG1 (Rhizobium meliloti (strain 1021)) Explore Q92MG1 Go to UniProtKB: Q92MG1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92MG1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP 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]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TYR Query on TYR 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]	TYROSINE C₉ H₁₁ N O₃ OUYCCCASQSFEME-QMMMGPOBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [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: 1.40 Å
R-Value Free: 0.159 (Depositor), 0.158 (DCC)
R-Value Work: 0.115 (Depositor), 0.115 (DCC)
R-Value Observed: 0.117 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.409	α = 90
b = 68.891	β = 94.34
c = 51.097	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2014-10-22

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54-GM094662

Revision History (Full details and data files)

Version 1.0: 2014-10-22
Type: Initial release
Version 1.1: 2015-10-14
Changes: Data collection
Version 1.2: 2019-11-27
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-12-27
Changes: Data collection
Version 1.5: 2024-10-30
Changes: Structure summary