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- PDB-3vy8: Crystal Structure of PorB from Neisseria meningitidis in complex ... -

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Basic information

Entry
Database: PDB / ID: 3vy8
TitleCrystal Structure of PorB from Neisseria meningitidis in complex with Cesium ion, space group P63
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: 2.12 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)38,5784
Polymers38,1791
Non-polymers3993
Water1,67593
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)115,73412
Polymers114,5383
Non-polymers1,1969
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10570 Å2
ΔGint-295 kcal/mol
Surface area43900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.201, 83.201, 106.415
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11X-504-

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.: 3 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
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: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23050 / % possible obs: 97.4 % / Observed criterion σ(F): 16.5 / Observed criterion σ(I): 1.67
Reflection shellResolution: 2.1→2.15 Å / % possible all: 75.8

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Processing

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

3a2r
PDB Unreleased entry


Resolution: 2.12→42.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 16.5 / ESU R: 0.226 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2535 1091 4.7 %RANDOM
Rwork0.21017 ---
obs0.21233 21933 96.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å2-0 Å2
2--0.1 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.12→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 3 93 2689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192673
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.923609
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7225344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33724.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.315433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.441514
X-RAY DIFFRACTIONr_chiral_restr0.1370.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022081
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.118→2.173 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 75 -
Rwork0.335 1117 -
obs--68.78 %

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