3EGW | pdb_00003egw

The crystal structure of the NarGHI mutant NarH - C16A

PDB DOI: https://doi.org/10.2210/pdb3EGW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2008-09-11 Released: 2010-03-02
Deposition Author(s): Bertero, M.G., Rothery, R.A., Weiner, J.H., Strynadka, N.C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.196 (Depositor), 0.199 (DCC)
R-Value Work:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

When width is more important than height: Barriers to electron transfer in E.coli nitrate reductase

Parkin, A., Blanford, C.F., Rothery, R.A., Macey, R., Bertero, M., Strynadka, N.C.J., Armstrong, F.A., Weiner, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 228.97 kDa
Atom Count: 17,504
Modeled Residue Count: 1,978
Deposited Residue Count: 1,978
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Respiratory nitrate reductase 1 alpha chain	A	1,244	Escherichia coli K-12	Mutation(s): 0 Gene Names: narG, bisD, narC, b1224, JW1215 EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P09152 (Escherichia coli (strain K12)) Explore P09152 Go to UniProtKB: P09152
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09152
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Respiratory nitrate reductase 1 beta chain	B	509	Escherichia coli K-12	Mutation(s): 1 Gene Names: narH, b1225, JW1216 EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P11349 (Escherichia coli (strain K12)) Explore P11349 Go to UniProtKB: P11349
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11349
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Respiratory nitrate reductase 1 gamma chain	C	225	Escherichia coli K-12	Mutation(s): 0 Gene Names: narI, chlI, b1227, JW1218 EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P11350 (Escherichia coli (strain K12)) Explore P11350 Go to UniProtKB: P11350
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11350
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD Query on MGD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MD1 Query on MD1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ IRGDLSAXQOKWLX-XHEYTWMPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
3PH Query on 3PH Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	M [auth C], N [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain M [auth C] Focus chain N [auth C]
AGA Query on AGA Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE C₁₉ H₃₆ O₁₀ P UQSXQYRZHMGKIE-DLBZAZTESA-M		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	G [auth A], I [auth B], J [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] mmCIF format, chain H [auth B] mmCIF format, chain K [auth B]	H [auth B], K [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth B] Interactions & Density Focus chain H [auth B] Focus chain K [auth B]
6MO Query on 6MO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MOLYBDENUM(VI) ION Mo HCNGUXXTNNIKCQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]