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- PDB-5c6p: protein C -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5c6p
Titleprotein C
Components
  • protein C
  • protein D
KeywordsTRANSPORT PROTEIN / protein
Function / homology
Function and homology information


antiporter activity / xenobiotic transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function
Multi antimicrobial extrusion protein / MatE / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Multi antimicrobial extrusion protein / MatE / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-4YH / Protein B / Multidrug transporter
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsLu, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094195 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for the blockade of MATE multidrug efflux pumps.
Authors: Radchenko, M. / Symersky, J. / Nie, R. / Lu, M.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein C
B: protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0893
Polymers60,6352
Non-polymers4551
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.642, 117.642, 225.989
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein protein C / / Putative efflux pump protein


Mass: 49717.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: NGO0395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F9J8
#2: Protein protein D


Mass: 10916.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: M1E1G6
#3: Chemical ChemComp-4YH / (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl)pentanenitrile


Mass: 454.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38N2O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 7.45 Å3/Da / Density % sol: 83.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 33124 / % possible obs: 91 % / Redundancy: 6 % / Net I/σ(I): 20

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 3→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.29 --
Rwork0.28 --
obs-31380 91 %
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 33 0 4248

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