2YF2

Crystal structure of the oligomerisation domain of C4b-binding protein from Gallus gallus

PDB DOI: https://doi.org/10.2210/pdb2YF2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Gallus gallus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-04-01 Released: 2012-04-18
Deposition Author(s): Caesar, J.J.E., Hill, F., Lea, S.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.236
R-Value Work: 0.220
R-Value Observed: 0.221

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the Oligomerisation Domain of C4B-Binding Protein from Gallus Gallus

Caesar, J.J.E., Hill, F., Lea, S.M.

To be published.

Macromolecule Content

Total Structure Weight: 52.96 kDa
Atom Count: 3,073
Modelled Residue Count: 364
Deposited Residue Count: 455
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4B BINDING PROTEIN	A, B, C, D, E A, B, C, D, E, F, G	65	Gallus gallus	Mutation(s): 1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain GA [auth G] SDF format, chain H [auth A] SDF format, chain HA [auth G] SDF format, chain IA [auth G] SDF format, chain J [auth B] SDF format, chain JA [auth G] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth B] MOL2 format, chain JA [auth G] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain J [auth B] mmCIF format, chain JA [auth G] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	CA [auth F] DA [auth F] EA [auth F] GA [auth G] H [auth A] CA [auth F], DA [auth F], EA [auth F], GA [auth G], H [auth A], HA [auth G], IA [auth G], J [auth B], JA [auth G], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain H [auth A] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth B] Focus chain JA [auth G] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain H [auth A] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth B] Focus chain JA [auth G] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain I [auth A] SDF format, chain KA [auth G] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth E] BA [auth E] FA [auth F] I [auth A] KA [auth G] AA [auth E], BA [auth E], FA [auth F], I [auth A], KA [auth G], P [auth B], Q [auth B], R [auth B], V [auth C], Y [auth D], Z [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain KA [auth G] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain KA [auth G] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.236
R-Value Work: 0.220
R-Value Observed: 0.221
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.888	α = 90
b = 140.238	β = 90
c = 85.465	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-04-18

Deposition Author(s):

Caesar, J.J.E.

Hill, F.

Lea, S.M.

Revision History (Full details and data files)

Version 1.0: 2012-04-18
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Other, Structure summary