3S2F | pdb_00003s2f

Crystal Structure of FurX NADH:Furfural

PDB DOI: https://doi.org/10.2210/pdb3S2F/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cupriavidus pinatubonensis JMP134
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-16 Released: 2012-06-13
Deposition Author(s): Hayes, R., Sanchez, E.J., Webb, B.N., Hooper, T., Nissen, M.S., Li, Q., Xun, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.214 (Depositor), 0.211 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures and furfural reduction mechanism of a bacterial zinc-dependent alcohol dehydrogenase

Hayes, R., Sanchez, E.J., Webb, B.N., Hooper, T., Nissen, M.S., Li, Q., Xun, L.

To be published.

Macromolecule Content

Total Structure Weight: 292.09 kDa
Atom Count: 22,651
Modeled Residue Count: 2,720
Deposited Residue Count: 2,720
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-containing alcohol dehydrogenase superfamily	A, B, C, D, E A, B, C, D, E, F, G, H	340	Cupriavidus pinatubonensis JMP134	Mutation(s): 0 Gene Names: Reut_B3677 EC: 1.1.1.1
UniProt
Find proteins for Q46UZ9 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46UZ9 Go to UniProtKB: Q46UZ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46UZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain VA [auth H] SDF format, chain MA [auth G] SDF format, chain JA [auth F] SDF format, chain EA [auth E] MOL2 format, chain VA [auth H] MOL2 format, chain MA [auth G] MOL2 format, chain JA [auth F] MOL2 format, chain EA [auth E] mmCIF format, chain VA [auth H] mmCIF format, chain MA [auth G] mmCIF format, chain JA [auth F] mmCIF format, chain EA [auth E]	EA [auth E], JA [auth F], MA [auth G], VA [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain EA [auth E] Focus chain JA [auth F] Focus chain MA [auth G] Focus chain VA [auth H] Interactions & Density Focus chain EA [auth E] Focus chain JA [auth F] Focus chain MA [auth G] Focus chain VA [auth H]
ISP Query on ISP Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain K [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A]	K [auth A], P [auth B], U [auth C], Z [auth D]	PHOSPHORYLISOPROPANE C₃ H₉ O₄ P QPPQHRDVPBTVEV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]
FU2 Query on FU2 Download:Ideal Coordinates CCD File SDF format, chain SA [auth H] SDF format, chain PA [auth G] SDF format, chain KA [auth F] SDF format, chain FA [auth E] MOL2 format, chain SA [auth H] MOL2 format, chain PA [auth G] MOL2 format, chain KA [auth F] MOL2 format, chain FA [auth E] mmCIF format, chain SA [auth H] mmCIF format, chain PA [auth G] mmCIF format, chain KA [auth F] mmCIF format, chain FA [auth E]	FA [auth E], KA [auth F], PA [auth G], SA [auth H]	FURFURAL C₅ H₄ O₂ HYBBIBNJHNGZAN-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain KA [auth F] Focus chain PA [auth G] Focus chain SA [auth H] Interactions & Density Focus chain FA [auth E] Focus chain KA [auth F] Focus chain PA [auth G] Focus chain SA [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain XA [auth H] SDF format, chain WA [auth H] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain RA [auth G] SDF format, chain R [auth B] SDF format, chain QA [auth G] SDF format, chain Q [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth F] SDF format, chain L [auth A] SDF format, chain GA [auth E] SDF format, chain BA [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain XA [auth H] MOL2 format, chain WA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain XA [auth H] mmCIF format, chain WA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain BA [auth D]	AA [auth D] BA [auth D] GA [auth E] L [auth A] LA [auth F] AA [auth D], BA [auth D], GA [auth E], L [auth A], LA [auth F], M [auth A], Q [auth B], QA [auth G], R [auth B], RA [auth G], V [auth C], W [auth C], WA [auth H], XA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth E] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth H] Focus chain XA [auth H] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth E] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth H] Focus chain XA [auth H]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain UA [auth H] SDF format, chain TA [auth H] SDF format, chain OA [auth G] SDF format, chain O [auth B] SDF format, chain NA [auth G] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth F] SDF format, chain DA [auth E] SDF format, chain CA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain UA [auth H] MOL2 format, chain TA [auth H] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain UA [auth H] mmCIF format, chain TA [auth H] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E]	CA [auth E] DA [auth E] HA [auth F] I [auth A] IA [auth F] CA [auth E], DA [auth E], HA [auth F], I [auth A], IA [auth F], J [auth A], N [auth B], NA [auth G], O [auth B], OA [auth G], S [auth C], T [auth C], TA [auth H], UA [auth H], X [auth D], Y [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain S [auth C] Focus chain T [auth C] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain S [auth C] Focus chain T [auth C] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214 (Depositor), 0.211 (DCC)
R-Value Work: 0.182 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.271	α = 106.08
b = 92.854	β = 89.97
c = 117.69	γ = 89.98

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations