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- PDB-3vy9: Crystal structure of PorB from Neisseria meningitidis in complex ... -

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Basic information

Entry
Database: PDB / ID: 3vy9
TitleCrystal structure of PorB from Neisseria meningitidis in complex with cesium ion, space group H32
ComponentsOuter membrane protein
KeywordsMEMBRANE PROTEIN / Beta-barrel / porin / channel / outer membrane protein
Function / homologyPorin / Porin / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsKattner, C. / Zaucha, J. / Jaenecke, F. / Zachariae, U. / Tanabe, M.
CitationJournal: Proteins / Year: 2013
Title: Identification of a cation transport pathway in Neisseria meningitidis PorB.
Authors: Kattner, C. / Zaucha, J. / Jaenecke, F. / Zachariae, U. / Tanabe, M.
History
DepositionSep 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7115
Polymers38,1791
Non-polymers5324
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Outer membrane protein
hetero molecules

X: Outer membrane protein
hetero molecules

X: Outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,13315
Polymers114,5383
Non-polymers1,59512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11320 Å2
ΔGint-409 kcal/mol
Surface area40790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.208, 144.208, 106.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11X-501-

HOH

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Components

#1: Protein Outer membrane protein


Mass: 38179.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: W135 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% Jeffamine M600, 50mM CsCl, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.63→81 Å / Num. obs: 11968 / % possible obs: 94.3 % / Observed criterion σ(F): 10.3 / Observed criterion σ(I): 1.86
Reflection shellResolution: 2.63→2.7 Å / % possible all: 76.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A2R

3a2r
PDB Unreleased entry


Resolution: 2.63→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.845 / Cross valid method: THROUGHOUT / σ(F): 10.3 / ESU R: 1.832 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28067 1192 10 %RANDOM
Rwork0.23538 ---
all0.23988 ---
obs0.23988 10770 93.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.341 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.63→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 4 12 2609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192642
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.9223562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6925340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30724.444126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.15315431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6381514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022047
LS refinement shellResolution: 2.632→2.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 70 -
Rwork0.342 599 -
obs--71.32 %

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