2WS3 | pdb_00002ws3

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD Tyr83Phe mutant

PDB DOI: https://doi.org/10.2210/pdb2WS3/pdb

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

Deposited: 2009-09-03 Released: 2010-08-25
Deposition Author(s): Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.253 (Depositor), 0.243 (DCC)
R-Value Work:
0.219 (Depositor), 0.210 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Succinate Dehydrogenase Activity

Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

To be published.

Macromolecule Content

Total Structure Weight: 363.27 kDa
Atom Count: 24,900
Modeled Residue Count: 3,156
Deposited Residue Count: 3,210
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT	A, E, I	588	Escherichia coli	Mutation(s): 0 EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12)) Explore P0AC41 Go to UniProtKB: P0AC41
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AC41
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT	B, F, J	238	Escherichia coli	Mutation(s): 0 EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P07014 (Escherichia coli (strain K12)) Explore P07014 Go to UniProtKB: P07014
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07014
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT	C, G, K	129	Escherichia coli	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P69054 (Escherichia coli (strain K12)) Explore P69054 Go to UniProtKB: P69054
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69054
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT	D, H, L	115	Escherichia coli	Mutation(s): 1 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12)) Explore P0AC44 Go to UniProtKB: P0AC44
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AC44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain M [auth A] SDF format, chain U [auth E] MOL2 format, chain CA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain U [auth E] mmCIF format, chain CA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain U [auth E]	CA [auth I], M [auth A], U [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain CA [auth I] Focus chain M [auth A] Focus chain U [auth E] Interactions & Density Focus chain CA [auth I] Focus chain M [auth A] Focus chain U [auth E]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain T [auth C] SDF format, chain JA [auth K] MOL2 format, chain BA [auth G] MOL2 format, chain T [auth C] MOL2 format, chain JA [auth K] mmCIF format, chain BA [auth G] mmCIF format, chain T [auth C] mmCIF format, chain JA [auth K]	BA [auth G], JA [auth K], T [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth G] Focus chain JA [auth K] Focus chain T [auth C] Interactions & Density Focus chain BA [auth G] Focus chain JA [auth K] Focus chain T [auth C]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain Q [auth B] SDF format, chain GA [auth J] MOL2 format, chain Y [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain GA [auth J] mmCIF format, chain Y [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain GA [auth J]	GA [auth J], Q [auth B], Y [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain GA [auth J] Focus chain Q [auth B] Focus chain Y [auth F] Interactions & Density Focus chain GA [auth J] Focus chain Q [auth B] Focus chain Y [auth F]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Z [auth F] SDF format, chain HA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth F] MOL2 format, chain HA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth F] mmCIF format, chain HA [auth J]	HA [auth J], R [auth B], Z [auth F]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain HA [auth J] Focus chain R [auth B] Focus chain Z [auth F] Interactions & Density Focus chain HA [auth J] Focus chain R [auth B] Focus chain Z [auth F]
CBE Query on CBE Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain IA [auth K] SDF format, chain S [auth C] MOL2 format, chain AA [auth G] MOL2 format, chain IA [auth K] MOL2 format, chain S [auth C] mmCIF format, chain AA [auth G] mmCIF format, chain IA [auth K] mmCIF format, chain S [auth C]	AA [auth G], IA [auth K], S [auth C]	2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE C₁₂ H₁₃ N O₂ S GYSSRZJIHXQEHQ-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain IA [auth K] Focus chain S [auth C] Interactions & Density Focus chain AA [auth G] Focus chain IA [auth K] Focus chain S [auth C]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain FA [auth J] SDF format, chain X [auth F] SDF format, chain P [auth B] MOL2 format, chain FA [auth J] MOL2 format, chain X [auth F] MOL2 format, chain P [auth B] mmCIF format, chain FA [auth J] mmCIF format, chain X [auth F] mmCIF format, chain P [auth B]	FA [auth J], P [auth B], X [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain FA [auth J] Focus chain P [auth B] Focus chain X [auth F] Interactions & Density Focus chain FA [auth J] Focus chain P [auth B] Focus chain X [auth F]
TEO Query on TEO Download:Ideal Coordinates CCD File SDF format, chain EA [auth I] SDF format, chain O [auth A] SDF format, chain W [auth E] MOL2 format, chain EA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain W [auth E] mmCIF format, chain EA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain W [auth E]	EA [auth I], O [auth A], W [auth E]	MALATE LIKE INTERMEDIATE C₄ H₄ O₅ QFBHYOKSQPPXHZ-UWTATZPHSA-L		Interactions Focus chain EA [auth I] Focus chain O [auth A] Focus chain W [auth E] Interactions & Density Focus chain EA [auth I] Focus chain O [auth A] Focus chain W [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain DA [auth I] SDF format, chain N [auth A] SDF format, chain V [auth E] MOL2 format, chain DA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain V [auth E] mmCIF format, chain DA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain V [auth E]	DA [auth I], N [auth A], V [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain DA [auth I] Focus chain N [auth A] Focus chain V [auth E] Interactions & Density Focus chain DA [auth I] Focus chain N [auth A] Focus chain V [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.253 (Depositor), 0.243 (DCC)
R-Value Work: 0.219 (Depositor), 0.210 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.85	α = 90
b = 184.71	β = 90
c = 203.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description