2D4E | pdb_00002d4e

Crystal Structure of the HpcC from Thermus Thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb2D4E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-10-18 Released: 2006-04-18
Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.212 (Depositor), 0.211 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the HpcC from Thermus Thermophilus HB8

Mizutani, H., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 230.87 kDa
Atom Count: 17,834
Modeled Residue Count: 2,056
Deposited Residue Count: 2,060
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase	A, B, C, D	515	Thermus thermophilus HB8	Mutation(s): 0 EC: 1.2.1.60
UniProt
Find proteins for Q5SJP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJP9 Go to UniProtKB: Q5SJP9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJP9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth C] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C]	K [auth C], O [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain K [auth C] Focus chain O [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	E [auth A] G [auth B] I [auth C] J [auth C] M [auth D] E [auth A], G [auth B], I [auth C], J [auth C], M [auth D], N [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.212 (Depositor), 0.211 (DCC)
R-Value Work: 0.179 (Depositor), 0.179 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.202	α = 103.97
b = 95.086	β = 116.11
c = 98.835	γ = 104.44

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-04-18

Deposition Author(s):

Mizutani, H.

Kunishima, N.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-04-18
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

2D4E | pdb_00002d4e

Crystal Structure of the HpcC from Thermus Thermophilus HB8

Literature

Crystal Structure of the HpcC from Thermus Thermophilus HB8

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)