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- PDB-2brr: Complex of the neisserial PorA P1.4 epitope peptide and two Fab- ... -

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Basic information

Entry
Database: PDB / ID: 2brr
TitleComplex of the neisserial PorA P1.4 epitope peptide and two Fab- fragments (antibody MN20B9.34)
Components
  • (MN20B9.34 ANTI-P1.4 ANTIBODY, FAB ...) x 2
  • CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / ANTI-PORA ANTIBODY / P1.4 ANTIBODY / ANTIGEN / PORIN / TRANSMEMBRANE / ANTIBODY-ANTIGEN COMPLEX
Function / homology
Function and homology information


porin activity / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Gram-negative porin / Porin, Gram-negative type / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Class 1 outer membrane protein variable region 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
NEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOomen, C.J. / Hoogerhout, P. / Kuipers, B. / Vidarsson, G. / Van Alphen, L. / Gros, P.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of an Anti-Meningococcal Subtype P1.4 Pora Antibody Provides Basis for Peptide- Vaccine Design.
Authors: Oomen, C.J. / Hoogerhout, P. / Kuipers, B. / Vidarsson, G. / Van Alphen, L. / Gros, P.
History
DepositionMay 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 16, 2012Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: MN20B9.34 ANTI-P1.4 ANTIBODY, FAB HEAVY CHAIN
L: MN20B9.34 ANTI-P1.4 ANTIBODY, FAB LIGHT CHAIN
P: CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2
X: MN20B9.34 ANTI-P1.4 ANTIBODY, FAB LIGHT CHAIN
Y: MN20B9.34 ANTI-P1.4 ANTIBODY, FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0588
Polymers96,8065
Non-polymers2523
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-77 kcal/mol
Surface area46130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.666, 63.833, 124.701
Angle α, β, γ (deg.)90.00, 86.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21L
12Y
22H
13X
23L
14Y
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116X109 - 214
2116L109 - 214
1126Y114 - 215
2126H114 - 215
1136X2 - 108
2136L2 - 108
1146Y1 - 113
2146H1 - 113

NCS ensembles :
ID
1
2
3
4
DetailsTHE PENTAMERIC ASSEMBLY DESCRIBED HERE IS COMPOSED OF TWO HEAVY/LIGHT CHAIN DIMERS, BOTH BOUND TO THE SINGLE CHAIN P.CHAINS H AND L ARE MARGINALLY MORE TIGHTLY BOUND TO THE PEPTIDE THAN CHAINS X AND Y

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2


Mass: 1244.445 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR LOOP 4 OF PORA SUBTYPE P1.4, RESIDUES 16-26
Source method: obtained synthetically / Details: N-TERMINUS ACETYLATED, C-TERMINUS AMIDATED / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria) / References: UniProt: Q51183

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Antibody , 2 types, 4 molecules HYLX

#1: Antibody MN20B9.34 ANTI-P1.4 ANTIBODY, FAB HEAVY CHAIN


Mass: 24353.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: MN20B9.34 MURINE HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#2: Antibody MN20B9.34 ANTI-P1.4 ANTIBODY, FAB LIGHT CHAIN


Mass: 23427.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: MN20B9.34 MURINE HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)

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Non-polymers , 3 types, 290 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF CHAIN P IS GIVEN BY GENBANK ENTRY CAA78633

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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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 4
Details: 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE/ACETIC ACID (PH 4.0) AND 25% W/V PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9315
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9315 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 60806 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CE1

1ce1


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.458 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3002 5.1 %RANDOM
Rwork0.198 ---
obs0.2 56219 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0.11 Å2
2--1.14 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6757 0 14 287 7058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9459488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74724.498269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.671151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6811518
X-RAY DIFFRACTIONr_chiral_restr0.090.21047
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025276
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.22895
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24694
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2418
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7851.54510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24227146
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89832877
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7084.52342
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11X811loose positional0.335
12L811loose positional0.335
21Y738loose positional0.445
22H738loose positional0.445
31X809loose positional0.395
32L809loose positional0.395
41Y971loose positional0.515
42H971loose positional0.515
11X811loose thermal1.3810
12L811loose thermal1.3810
21Y738loose thermal2.1910
22H738loose thermal2.1910
31X809loose thermal1.0610
32L809loose thermal1.0610
41Y971loose thermal1.3110
42H971loose thermal1.3110
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.281 180
Rwork0.221 3985
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.13820.03420.1220.39040.11741.26240.0691-0.1509-0.23650.0799-0.0516-0.02880.0768-0.1192-0.0175-0.0196-0.0145-0.0225-0.03910.0371-0.061855.47910.614135.166
22.50980.14280.17690.45770.47292.2736-0.12240.215-0.0569-0.0330.1142-0.0069-0.19310.2510.0082-0.0455-0.0487-0.0118-0.0259-0.0044-0.122470.7899.703173.306
32.0349-0.12330.29460.48750.13951.3979-0.0043-0.00090.05380.0312-0.01570.01360.0448-0.05010.02-0.06550.0072-0.0072-0.05460.014-0.080244.90410.144101.589
41.704-0.2994-0.44490.4238-0.20171.83140.04540.22840.0609-0.0866-0.0083-0.01280.0846-0.0271-0.0371-0.03920.0038-0.0122-0.00540.0107-0.073880.29311.65207.022
50.0869-0.05631.37890.0366-0.917228.93960.01550.5480.18660.04530.1633-0.0492-0.21890.2376-0.17880.0533-0.0888-0.08240.12740.0915-0.088965.15817.68154.614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 108
2X-RAY DIFFRACTION1Y1 - 113
3X-RAY DIFFRACTION2L1 - 108
4X-RAY DIFFRACTION2H1 - 113
5X-RAY DIFFRACTION3X109 - 214
6X-RAY DIFFRACTION3Y114 - 215
7X-RAY DIFFRACTION4L109 - 214
8X-RAY DIFFRACTION4H114 - 215
9X-RAY DIFFRACTION5P3 - 11

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