1Z1N

Crystal Structure of the sixteen heme cytochrome from Desulfovibrio gigas

PDB DOI: https://doi.org/10.2210/pdb1Z1N/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Megalodesulfovibrio gigas
Mutation(s): No

Deposited: 2005-03-04 Released: 2006-04-04
Deposition Author(s): Santos-Silva, T., Dias, J.M., Romao, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.260
R-Value Work: 0.194
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 71.03 kDa
Atom Count: 4,998
Modelled Residue Count: 516
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sixteen heme cytochrome	A [auth X]	560	Megalodesulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for T2G9Q2 (Megalodesulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759)) Explore T2G9Q2 Go to UniProtKB: T2G9Q2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	T2G9Q2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-allopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth A]	2		N-Glycosylation	Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
Glycosylation Resources
GlyTouCan: G43875TD GlyCosmos: G43875TD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain F [auth X] SDF format, chain G [auth X] SDF format, chain H [auth X] SDF format, chain I [auth X] SDF format, chain J [auth X] SDF format, chain K [auth X] SDF format, chain L [auth X] SDF format, chain M [auth X] SDF format, chain N [auth X] SDF format, chain O [auth X] SDF format, chain P [auth X] SDF format, chain Q [auth X] SDF format, chain R [auth X] SDF format, chain S [auth X] SDF format, chain T [auth X] SDF format, chain U [auth X] MOL2 format, chain F [auth X] MOL2 format, chain G [auth X] MOL2 format, chain H [auth X] MOL2 format, chain I [auth X] MOL2 format, chain J [auth X] MOL2 format, chain K [auth X] MOL2 format, chain L [auth X] MOL2 format, chain M [auth X] MOL2 format, chain N [auth X] MOL2 format, chain O [auth X] MOL2 format, chain P [auth X] MOL2 format, chain Q [auth X] MOL2 format, chain R [auth X] MOL2 format, chain S [auth X] MOL2 format, chain T [auth X] MOL2 format, chain U [auth X]	F [auth X] G [auth X] H [auth X] I [auth X] J [auth X] F [auth X], G [auth X], H [auth X], I [auth X], J [auth X], K [auth X], L [auth X], M [auth X], N [auth X], O [auth X], P [auth X], Q [auth X], R [auth X], S [auth X], T [auth X], U [auth X]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Focus chain P [auth X] Focus chain Q [auth X] Focus chain R [auth X] Focus chain S [auth X] Focus chain T [auth X] Focus chain U [auth X] Interactions & Density Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Focus chain P [auth X] Focus chain Q [auth X] Focus chain R [auth X] Focus chain S [auth X] Focus chain T [auth X] Focus chain U [auth X]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain V [auth X] SDF format, chain W [auth X] SDF format, chain X SDF format, chain Y [auth X] SDF format, chain Z [auth X] MOL2 format, chain V [auth X] MOL2 format, chain W [auth X] MOL2 format, chain X MOL2 format, chain Y [auth X] MOL2 format, chain Z [auth X]	V [auth X], W [auth X], X, Y [auth X], Z [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain V [auth X] Focus chain W [auth X] Focus chain X Focus chain Y [auth X] Focus chain Z [auth X] Interactions & Density Focus chain V [auth X] Focus chain W [auth X] Focus chain X Focus chain Y [auth X] Focus chain Z [auth X]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain D [auth X] SDF format, chain E [auth X] MOL2 format, chain C [auth X] MOL2 format, chain D [auth X] MOL2 format, chain E [auth X]	C [auth X], D [auth X], E [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Interactions & Density Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.260
R-Value Work: 0.194
R-Value Observed: 0.195
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.889	α = 90
b = 90.799	β = 90
c = 83.934	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-04-04

Deposition Author(s):

Santos-Silva, T.

Dias, J.M.

Romao, M.J.

Revision History (Full details and data files)

Version 1.0: 2006-04-04
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary