1XC1 | pdb_00001xc1

Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (FBP)

PDB DOI: https://doi.org/10.2210/pdb1XC1/pdb

Classification: METAL TRANSPORT
Organism(s): Neisseria gonorrhoeae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-08-31 Released: 2004-09-21
Deposition Author(s): Zhong, W., Alexeev, D., Harvey, I., Guo, M., Hunter, D.J.B., Zhu, H., Campopiano, D.J., Sadler, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.275 (Depositor)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Assembly of an Oxo-Zirconium(IV) Cluster in a Protein Cleft

Zhong, W., Alexeev, D., Harvey, I., Guo, M., Hunter, D.J.B., Zhu, H., Campopiano, D.J., Sadler, P.J.

(2004) Angew Chem Int Ed Engl 43: 5914-5918

PubMed: 15472987 Search on PubMed
DOI: https://doi.org/10.1002/anie.200460806
Primary Citation Related Structures:
1XC1

Organizational Affiliation

School of Chemistry, King's Buildings, The University of Edinburgh, West Mains Road, Edinburgh EH93JJ, UK.

Macromolecule Content

Total Structure Weight: 308.38 kDa
Atom Count: 22,547
Modeled Residue Count: 2,781
Deposited Residue Count: 2,781
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
periplasmic iron-binding protein	A, B, C, D, E A, B, C, D, E, F, G, H, I	309	Neisseria gonorrhoeae	Mutation(s): 0 Gene Names: FBPA
UniProt
Find proteins for P17259 (Neisseria gonorrhoeae) Explore P17259 Go to UniProtKB: P17259
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17259
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZRC Query on ZRC Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain P [auth G] SDF format, chain Q [auth H] SDF format, chain R [auth I] SDF format, chain O [auth F] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth A] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth I] MOL2 format, chain O [auth F] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] mmCIF format, chain M [auth D] mmCIF format, chain N [auth E] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth I] mmCIF format, chain O [auth F] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A]	J [auth A] K [auth B] L [auth C] M [auth D] N [auth E] J [auth A], K [auth B], L [auth C], M [auth D], N [auth E], O [auth F], P [auth G], Q [auth H], R [auth I]	OXO ZIRCONIUM(IV) CLUSTER O₁₇ P Zr₃ WBTZCCQRTTWINH-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.275 (Depositor)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.191 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.2	α = 90
b = 146.2	β = 90
c = 113.558	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-09-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description