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- PDB-1k24: Crystal Structure of the OpcA Outer Membrane Adhesin/Invasin from... -

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Basic information

Entry
Database: PDB / ID: 1k24
TitleCrystal Structure of the OpcA Outer Membrane Adhesin/Invasin from Neisseria meningitidis
Componentsouter membrane proteinVirulence-related outer membrane protein family
KeywordsMEMBRANE PROTEIN / Adhesin / Invasin / Outer Membrane / Beta Barrel
Function / homology
Function and homology information


aspartic-type endopeptidase activity / metal ion binding
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
OpcA protein / Outer membrane protein
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.03 Å
AuthorsPrince, S.M. / Achtman, M. / Derrick, J.P.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Expression, Refolding and Crystallization of the OpcA Invasin from Neisseria meningitidis
Authors: Prince, S.M. / Feron, C. / Janssens, D. / Lobet, Y. / Achtman, M. / Kusecek, B. / Bullough, P.A. / Derrick, J.P.
#2: Journal: J.EXP.MED. / Year: 1988
Title: Purification and Characterization of Eight Class 5 outer Membrane Protein Variants from a Clone of Neisseria meningitidis Serogroup A
Authors: Achtman, M. / Neilbert, M. / Crowe, B.A. / Strittmatter, W. / Kusecek, B. / Weyse, E. / Walsh, M.J. / Slawig, B. / Morelli, G. / Moll, A. / Blake, M.
#3: Journal: MOL.MICROBIOL. / Year: 1999
Title: Projection Structure of Reconstituted Opc Outer Membrane Protein from Neisseria meningitidis
Authors: Collins, R. / Achtman, M. / Ford, R. / Bullough, P. / Derrick, J.
#4: Journal: MOL.MICROBIOL. / Year: 1997
Title: Two-dimensional Structure of the Opc Invasin from Neisseria meningitidis
Authors: Merker, P. / Tommassen, J. / Kusacek, B. / Virji, M. / Sesardic, D. / Achtman, M.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7656
Polymers28,0931
Non-polymers6735
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: outer membrane protein
hetero molecules

A: outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,53112
Polymers56,1852
Non-polymers1,34610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3070 Å2
ΔGint-269 kcal/mol
Surface area27840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.859, 46.346, 73.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

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Components

#1: Protein outer membrane protein / Virulence-related outer membrane protein family / OpcA protein


Mass: 28092.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Outer membrane / Source: (natural) Neisseria meningitidis (bacteria) / References: UniProt: Q9AE79, UniProt: Q51227*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.04 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 6K, Zinc Acetate, Zinc Chloride, C10E5, Beta-heptyl-glucoside, TRIS/HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Prince, S.M., (2001) Acta Crystallogr., Sect.D, 57, 1164.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
180 %ethanol1drop
210 mg/mlprotein1drop
325 mMTris-HCl1droppH7.5
41 %(v/v)n-decylpentaoxyethylene1drop
550 mMTris acetic acid1reservoirpH7.5
6150 mMzinc acetate1reservoir
750 mM1reservoirZnCl2
80.5 %(w/v)n-heptyl beta-D-glucoside1reservoir
920 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 9, 1999 / Details: toroidal mirror
RadiationMonochromator: Diamond & Ge-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.03→36.5 Å / Num. all: 21875 / Num. obs: 21875 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 10.2 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 16.5
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1320 / Rsym value: 0.325 / % possible all: 82.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 36.4 Å / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Rmerge(I) obs: 0.325

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.03→36.5 Å / SU B: 4.423 / SU ML: 0.125
Isotropic thermal model: Overall Anisotropic B-factor applied. 28 TLS tensors refined, Residual B-factors also refined.
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.182 / Stereochemistry target values: Engh & Huber
Details: Maximum Likelihood target, Bulk Solvent Correction applied. TLS TENSORS WERE USED TO MODEL DISORDER, THE DEPOSITION CONTAINS THE EQUIVALENT B-FACTORS CALCULATED FROM THESE TENSORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1093 5 %Random
Rwork0.235 ---
all0.237 20754 --
obs0.237 20754 98.45 %-
Displacement parametersBiso mean: 70.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å2-1.58 Å2-1.67 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati sigma a0.182 Å0.203 Å
Refinement stepCycle: LAST / Resolution: 2.03→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 35 144 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.021
X-RAY DIFFRACTIONp_angle_d1.9511.954
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1550.5
X-RAY DIFFRACTIONp_plane_restr0.0050.02
X-RAY DIFFRACTIONp_chiral_restr0.1430.2
X-RAY DIFFRACTIONp_singtor_nbd5.3053
X-RAY DIFFRACTIONp_multtor_nbd19.87615
X-RAY DIFFRACTIONp_xyhbond_nbd0.2280.5
X-RAY DIFFRACTIONp_mcbond_it0.5671.5
X-RAY DIFFRACTIONp_mcangle_it0.9132
X-RAY DIFFRACTIONp_scbond_it1.6223
X-RAY DIFFRACTIONp_scangle_it2.4894.5
LS refinement shellResolution: 2.03→2.129 Å
RfactorNum. reflection
Rfree0.288 126
Rwork0.227 -
obs-2561
Refinement
*PLUS
Rfactor all: 0.237 / Rfactor obs: 0.235 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9511.954
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / Rfactor Rwork: 0.227 / Rfactor obs: 0.227

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