1WPB

Structure of Escherichia coli yfbU gene product

PDB DOI: https://doi.org/10.2210/pdb1WPB/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-09-01 Released: 2004-12-07
Deposition Author(s): Borek, D., Chen, Y., Zheng, M., Skarina, T., Savchenko, A., Edwards, A., Otwinowski, Z., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.227
R-Value Work: 0.190
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Escherichia coli yfbU gene product

Borek, D., Chen, Y., Zheng, M., Skarina, T., Savchenko, A., Edwards, A., Otwinowski, Z.

To be published.

Macromolecule Content

Total Structure Weight: 332.45 kDa
Atom Count: 24,406
Modelled Residue Count: 2,687
Deposited Residue Count: 2,752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein yfbU	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	172	Escherichia coli	Mutation(s): 0 Gene Names: yfbU
UniProt
Find proteins for Q1R9C1 (Escherichia coli (strain UTI89 / UPEC)) Explore Q1R9C1 Go to UniProtKB: Q1R9C1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1R9C1
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 AC [auth L] SDF format, chain DB [auth H] SDF format, chain DC [auth M] SDF format, chain EA [auth C] SDF format, chain EB [auth H] SDF format, chain EC [auth M] SDF format, chain FA [auth C] SDF format, chain FB [auth H] SDF format, chain FC [auth M] SDF format, chain HC [auth N] SDF format, chain IC [auth N] SDF format, chain JA [auth D] SDF format, chain JC [auth N] SDF format, chain KA [auth D] SDF format, chain KB [auth I] SDF format, chain KC [auth N] SDF format, chain LA [auth D] SDF format, chain LB [auth I] SDF format, chain MA [auth D] SDF format, chain NC [auth O] SDF format, chain OC [auth O] SDF format, chain PA [auth E] SDF format, chain PB [auth J] SDF format, chain QA [auth E] SDF format, chain QB [auth J] SDF format, chain QC [auth P] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain RC [auth P] SDF format, chain S [auth A] SDF format, chain SA [auth E] SDF format, chain TB [auth K] SDF format, chain U [auth B] SDF format, chain UB [auth K] SDF format, chain V [auth B] SDF format, chain VB [auth K] SDF format, chain W [auth B] SDF format, chain WA [auth F] SDF format, chain WB [auth K] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] SDF format, chain ZB [auth L] MOL2 format, chain AC [auth L] MOL2 format, chain DB [auth H] MOL2 format, chain DC [auth M] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth H] MOL2 format, chain EC [auth M] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth H] MOL2 format, chain FC [auth M] MOL2 format, chain HC [auth N] MOL2 format, chain IC [auth N] MOL2 format, chain JA [auth D] MOL2 format, chain JC [auth N] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth I] MOL2 format, chain KC [auth N] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth I] MOL2 format, chain MA [auth D] MOL2 format, chain NC [auth O] MOL2 format, chain OC [auth O] MOL2 format, chain PA [auth E] MOL2 format, chain PB [auth J] MOL2 format, chain QA [auth E] MOL2 format, chain QB [auth J] MOL2 format, chain QC [auth P] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain RC [auth P] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain TB [auth K] MOL2 format, chain U [auth B] MOL2 format, chain UB [auth K] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth K] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain WB [auth K] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G] MOL2 format, chain ZB [auth L]	AC [auth L] DB [auth H] DC [auth M] EA [auth C] EB [auth H] AC [auth L], DB [auth H], DC [auth M], EA [auth C], EB [auth H], EC [auth M], FA [auth C], FB [auth H], FC [auth M], HC [auth N], IC [auth N], JA [auth D], JC [auth N], KA [auth D], KB [auth I], KC [auth N], LA [auth D], LB [auth I], MA [auth D], NC [auth O], OC [auth O], PA [auth E], PB [auth J], QA [auth E], QB [auth J], QC [auth P], R [auth A], RA [auth E], RC [auth P], S [auth A], SA [auth E], TB [auth K], U [auth B], UB [auth K], V [auth B], VB [auth K], W [auth B], WA [auth F], WB [auth K], X [auth B], Y [auth B], YA [auth G], ZA [auth G], ZB [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AC [auth L] Focus chain DB [auth H] Focus chain DC [auth M] Focus chain EA [auth C] Focus chain EB [auth H] Focus chain EC [auth M] Focus chain FA [auth C] Focus chain FB [auth H] Focus chain FC [auth M] Focus chain HC [auth N] Focus chain IC [auth N] Focus chain JA [auth D] Focus chain JC [auth N] Focus chain KA [auth D] Focus chain KB [auth I] Focus chain KC [auth N] Focus chain LA [auth D] Focus chain LB [auth I] Focus chain MA [auth D] Focus chain NC [auth O] Focus chain OC [auth O] Focus chain PA [auth E] Focus chain PB [auth J] Focus chain QA [auth E] Focus chain QB [auth J] Focus chain QC [auth P] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RC [auth P] Focus chain S [auth A] Focus chain SA [auth E] Focus chain TB [auth K] Focus chain U [auth B] Focus chain UB [auth K] Focus chain V [auth B] Focus chain VB [auth K] Focus chain W [auth B] Focus chain WA [auth F] Focus chain WB [auth K] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth G] Focus chain ZA [auth G] Focus chain ZB [auth L] Interactions & Density Focus chain AC [auth L] Focus chain DB [auth H] Focus chain DC [auth M] Focus chain EA [auth C] Focus chain EB [auth H] Focus chain EC [auth M] Focus chain FA [auth C] Focus chain FB [auth H] Focus chain FC [auth M] Focus chain HC [auth N] Focus chain IC [auth N] Focus chain JA [auth D] Focus chain JC [auth N] Focus chain KA [auth D] Focus chain KB [auth I] Focus chain KC [auth N] Focus chain LA [auth D] Focus chain LB [auth I] Focus chain MA [auth D] Focus chain NC [auth O] Focus chain OC [auth O] Focus chain PA [auth E] Focus chain PB [auth J] Focus chain QA [auth E] Focus chain QB [auth J] Focus chain QC [auth P] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RC [auth P] Focus chain S [auth A] Focus chain SA [auth E] Focus chain TB [auth K] Focus chain U [auth B] Focus chain UB [auth K] Focus chain V [auth B] Focus chain VB [auth K] Focus chain W [auth B] Focus chain WA [auth F] Focus chain WB [auth K] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth G] Focus chain ZA [auth G] Focus chain ZB [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth H] SDF format, chain BA [auth C] SDF format, chain BB [auth H] SDF format, chain BC [auth M] SDF format, chain CA [auth C] SDF format, chain CB [auth H] SDF format, chain CC [auth M] SDF format, chain DA [auth C] SDF format, chain GA [auth D] SDF format, chain GB [auth I] SDF format, chain GC [auth N] SDF format, chain IA [auth D] SDF format, chain IB [auth I] SDF format, chain JB [auth I] SDF format, chain LC [auth O] SDF format, chain MB [auth J] SDF format, chain MC [auth O] SDF format, chain NA [auth E] SDF format, chain NB [auth J] SDF format, chain OA [auth E] SDF format, chain OB [auth J] SDF format, chain PC [auth P] SDF format, chain Q [auth A] SDF format, chain RB [auth K] SDF format, chain SB [auth K] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain XA [auth G] SDF format, chain XB [auth L] SDF format, chain YB [auth L] SDF format, chain Z [auth C] SDF format, chain HA [auth D] SDF format, chain HB [auth I] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain BC [auth M] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain CC [auth M] MOL2 format, chain DA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth I] MOL2 format, chain GC [auth N] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth I] MOL2 format, chain JB [auth I] MOL2 format, chain LC [auth O] MOL2 format, chain MB [auth J] MOL2 format, chain MC [auth O] MOL2 format, chain NA [auth E] MOL2 format, chain NB [auth J] MOL2 format, chain OA [auth E] MOL2 format, chain OB [auth J] MOL2 format, chain PC [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain RB [auth K] MOL2 format, chain SB [auth K] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain XA [auth G] MOL2 format, chain XB [auth L] MOL2 format, chain YB [auth L] MOL2 format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth I]	AA [auth C] AB [auth H] BA [auth C] BB [auth H] BC [auth M] AA [auth C], AB [auth H], BA [auth C], BB [auth H], BC [auth M], CA [auth C], CB [auth H], CC [auth M], DA [auth C], GA [auth D], GB [auth I], GC [auth N], HA [auth D], HB [auth I], IA [auth D], IB [auth I], JB [auth I], LC [auth O], MB [auth J], MC [auth O], NA [auth E], NB [auth J], OA [auth E], OB [auth J], PC [auth P], Q [auth A], RB [auth K], SB [auth K], T [auth B], TA [auth F], UA [auth F], VA [auth F], XA [auth G], XB [auth L], YB [auth L], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain BC [auth M] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain CC [auth M] Focus chain DA [auth C] Focus chain GA [auth D] Focus chain GB [auth I] Focus chain GC [auth N] Focus chain HA [auth D] Focus chain HB [auth I] Focus chain IA [auth D] Focus chain IB [auth I] Focus chain JB [auth I] Focus chain LC [auth O] Focus chain MB [auth J] Focus chain MC [auth O] Focus chain NA [auth E] Focus chain NB [auth J] Focus chain OA [auth E] Focus chain OB [auth J] Focus chain PC [auth P] Focus chain Q [auth A] Focus chain RB [auth K] Focus chain SB [auth K] Focus chain T [auth B] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain XA [auth G] Focus chain XB [auth L] Focus chain YB [auth L] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain BC [auth M] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain CC [auth M] Focus chain DA [auth C] Focus chain GA [auth D] Focus chain GB [auth I] Focus chain GC [auth N] Focus chain HA [auth D] Focus chain HB [auth I] Focus chain IA [auth D] Focus chain IB [auth I] Focus chain JB [auth I] Focus chain LC [auth O] Focus chain MB [auth J] Focus chain MC [auth O] Focus chain NA [auth E] Focus chain NB [auth J] Focus chain OA [auth E] Focus chain OB [auth J] Focus chain PC [auth P] Focus chain Q [auth A] Focus chain RB [auth K] Focus chain SB [auth K] Focus chain T [auth B] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain XA [auth G] Focus chain XB [auth L] Focus chain YB [auth L] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.227
R-Value Work: 0.190
R-Value Observed: 0.190
Space Group: P 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 230.521	α = 90
b = 230.521	β = 90
c = 230.521	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-12-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2004-12-07
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance