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- PDB-1yc9: The crystal structure of the outer membrane protein VceC from the... -

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Basic information

Entry
Database: PDB / ID: 1yc9
TitleThe crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 resolution
Componentsmultidrug resistance protein
KeywordsMEMBRANE PROTEIN / Vibrio cholerae / outer membrane protein / multidrug resistance
Function / homology
Function and homology information


response to xenobiotic stimulus => GO:0009410 / xenobiotic transmembrane transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / cell outer membrane / membrane => GO:0016020
Similarity search - Function
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Multidrug resistance protein, putative
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFederici, L. / Du, D. / Walas, F. / Matsumura, H. / Fernandez-Recio, J. / McKeegan, K.S. / Borges-Walmsley, M.I. / Luisi, B.F. / Walmsley, A.R.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The crystal structure of the outer membrane protein VCEC from the bacterial pathogen vibrio cholerae at 1.8 A resolution
Authors: Federici, L. / Du, D. / Walas, F. / Matsumura, H. / Fernandez-Recio, J. / McKeegan, K.S. / Borges-Walmsley, M.I. / Luisi, B.F. / Walmsley, A.R.
History
DepositionDec 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: multidrug resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3784
Polymers47,6851
Non-polymers6943
Water5,675315
1
A: multidrug resistance protein
hetero molecules

A: multidrug resistance protein
hetero molecules

A: multidrug resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,13512
Polymers143,0543
Non-polymers2,0819
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area16410 Å2
ΔGint-267 kcal/mol
Surface area54750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.458, 71.458, 190.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsBiological assembly is a trimer. Generate chain A by rotating: 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 and translating by: 0.0 0.0 0.0 Generate chain B. Rotate by: -0.5 -0.866 0.0 0.866 -0.5 0.0 0.0 0.0 1.0 Translate by: 1.0 1.0 0.0 Generate chain C. Rotate by: -0.5 0.866 0.0 -0.866 -0.5 0.0 0.0 0.0 1.0 Translate by: 0.0 1.0 0.0

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Components

#1: Protein multidrug resistance protein / VceC


Mass: 47684.824 Da / Num. of mol.: 1 / Mutation: E92C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: CVD101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KS51
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, Tris, NaCl, beta-DDM, octyl-beta-glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.8→63.6 Å / Num. all: 53358 / Num. obs: 53358 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.8 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→63.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.508 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22119 2708 5.1 %RANDOM
Rwork0.1887 ---
all0.19038 53358 --
obs0.19038 53358 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.748 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20.9 Å20 Å2
2--1.8 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→63.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 22 315 3462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213201
X-RAY DIFFRACTIONr_bond_other_d0.0020.022899
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9434361
X-RAY DIFFRACTIONr_angle_other_deg1.05536702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8325419
X-RAY DIFFRACTIONr_chiral_restr0.2540.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023680
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02647
X-RAY DIFFRACTIONr_nbd_refined0.2190.2762
X-RAY DIFFRACTIONr_nbd_other0.2580.23320
X-RAY DIFFRACTIONr_nbtor_other0.0910.21921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.2144
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.243
X-RAY DIFFRACTIONr_mcbond_it1.0891.52048
X-RAY DIFFRACTIONr_mcangle_it1.93923233
X-RAY DIFFRACTIONr_scbond_it3.20231153
X-RAY DIFFRACTIONr_scangle_it5.1754.51123
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 175
Rwork0.272 3703

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