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- PDB-2vdf: Structure of the OpcA adhesion from Neisseria meningitidis determ... -

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Basic information

Entry
Database: PDB / ID: 2vdf
TitleStructure of the OpcA adhesion from Neisseria meningitidis determined by crystallization from the cubic mesophase
ComponentsOUTER MEMBRANE PROTEINVirulence-related outer membrane protein family
KeywordsMEMBRANE PROTEIN / INVASIN / ADHESIN / BETA BARREL / OUTER MEMBRANE
Function / homology
Function and homology information


aspartic-type endopeptidase activity
Similarity search - Function
OPCA outer membrane adhesin/invasin / Outer membrane adhesin OpcA / Outer membrane protein OpcA / Outer membrane adhesin/peptidase omptin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-OCTANE / Outer membrane protein
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCherezov, V. / Liu, W. / Derrick, J.P. / Luan, B. / Aksimentiev, A. / Katritch, V. / Caffrey, M.
Citation
Journal: Proteins / Year: 2008
Title: In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin.
Authors: Cherezov, V. / Liu, W. / Derrick, J.P. / Luan, B. / Aksimentiev, A. / Katritch, V. / Caffrey, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal Structure of the Opca Integral Membrane Adhesin from Neisseria Meningitidis.
Authors: Prince, S.M. / Achtman, M. / Derrick, J.P.
History
DepositionOct 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / exptl_crystal_grow / reflns
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3033
Polymers28,0931
Non-polymers2102
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.860, 42.500, 150.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OUTER MEMBRANE PROTEIN / Virulence-related outer membrane protein family / OPCA


Mass: 28092.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9AE79
#2: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSULFATE ION (SO4): FROM CRYSTALLIZATION CONDITIONS N-OCTANE (OCT): ORIGINATES FROM DETERGENT USED ...SULFATE ION (SO4): FROM CRYSTALLIZATION CONDITIONS N-OCTANE (OCT): ORIGINATES FROM DETERGENT USED IN CRYSTALLIZATION. DENSITY FOR HEADGROUP NOT OBSERVED.

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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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 18%(V/V) PEG400, 0.1 M POTASSIUM SULFATE, 0.05 M HEPES, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9176
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9176 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 18131 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K24

1k24


Resolution: 1.95→10 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.889 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 927 5.2 %RANDOM
Rwork0.224 ---
obs0.227 17043 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 13 120 1900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9532432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4235220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54523.90282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39115318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7211511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021346
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.3690
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.51202
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.373
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.440.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9851.51131
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.20821762
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.6473769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.0614.5670
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 59
Rwork0.224 1218

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