1Z1N | pdb_00001z1n

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 (Depositor), 0.265 (DCC)
R-Value Work:
0.194 (Depositor), 0.204 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.0 of the entry. See complete history.

Literature

Crystal Structure of the sixteen heme cytochrome from Desulfovibrio gigas

Santos-Silva, T., Dias, J.M., Romao, M.J.

To be published.

Macromolecule Content

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

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T2G9Q2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth X]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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] mmCIF format, chain F [auth X] mmCIF format, chain G [auth X] mmCIF format, chain H [auth X] mmCIF format, chain I [auth X] mmCIF format, chain J [auth X] mmCIF format, chain K [auth X] mmCIF format, chain L [auth X] mmCIF format, chain M [auth X] mmCIF format, chain N [auth X] mmCIF format, chain O [auth X] mmCIF format, chain P [auth X] mmCIF format, chain Q [auth X] mmCIF format, chain R [auth X] mmCIF format, chain S [auth X] mmCIF format, chain T [auth X] mmCIF 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] mmCIF format, chain V [auth X] mmCIF format, chain W [auth X] mmCIF format, chain X mmCIF format, chain Y [auth X] mmCIF 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] mmCIF format, chain C [auth X] mmCIF format, chain D [auth X] mmCIF 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 (Depositor), 0.265 (DCC)
R-Value Work: 0.194 (Depositor), 0.204 (DCC)
R-Value Observed: 0.195 (Depositor)

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

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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
Version 3.0: 2024-12-25
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary