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- PDB-1uwx: P1.2 serosubtype antigen derived from N. meningitidis PorA in com... -

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Basic information

Entry
Database: PDB / ID: 1uwx
TitleP1.2 serosubtype antigen derived from N. meningitidis PorA in complex with Fab fragment
Components
  • (ANTIBODY) x 2
  • CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2
  • PROTEIN G-PRIME
KeywordsIMMUNE SYSTEM / ANTIBODY-COMPLEX / FAB / IMMUNOGLOBULIN / PROTEIN G / PORA / ANTIBODY / IGB
Function / homology
Function and homology information


IgG binding / porin activity / pore complex / B cell differentiation / cell outer membrane / monoatomic ion transmembrane transport / extracellular region / plasma membrane
Similarity search - Function
Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / : / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 ...Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / : / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Porin domain superfamily / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin G-binding protein G / Class 1 outer membrane protein variable region 2 / Protein G' / Major outer membrane protein IA
Similarity search - Component
Biological speciesSTREPTOCOCCUS SP. (bacteria)
MUS MUSCULUS (house mouse)
NEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTzitzilonis, C. / Prince, S.M. / Collins, R.F. / Maiden, M.C.J. / Feavers, I.M. / Derrick, J.P.
CitationJournal: Proteins: Struct., Funct., Bioinf. / Year: 2005
Title: Structural Variation and Immune Recognition of the P1.2 Subtype Meningococcal Antigen.
Authors: Tzitzilonis, C. / Prince, S.M. / Collins, R.F. / Achtman, M. / Feavers, I.M. / Maiden, M.C.J. / Derrick, J.P.
History
DepositionFeb 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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
A: PROTEIN G-PRIME
B: PROTEIN G-PRIME
H: ANTIBODY
K: ANTIBODY
L: ANTIBODY
M: ANTIBODY
P: CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2
Q: CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2


Theoretical massNumber of molelcules
Total (without water)112,2718
Polymers112,2718
Non-polymers00
Water7,116395
1
A: PROTEIN G-PRIME
H: ANTIBODY
L: ANTIBODY
P: CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2


Theoretical massNumber of molelcules
Total (without water)56,1354
Polymers56,1354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-52.4 kcal/mol
Surface area28310 Å2
MethodPISA
2
B: PROTEIN G-PRIME
K: ANTIBODY
M: ANTIBODY
Q: CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2


Theoretical massNumber of molelcules
Total (without water)56,1354
Polymers56,1354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-52.6 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.426, 110.568, 138.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21K
12H
22M
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112L1 - 213
2112K1 - 213
1121H1 - 104
2121M1 - 104
1221H2 - 223
2221M2 - 223
1132A5 - 62
2132B5 - 62

NCS ensembles :
ID
1
2
3

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Components

#1: Protein PROTEIN G-PRIME


Mass: 6881.566 Da / Num. of mol.: 2 / Fragment: RESIDUES 56-118 (DOMAIN II)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS SP. (bacteria) / Description: HYBRIDOMA / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q54181, UniProt: P19909*PLUS
#2: Antibody ANTIBODY


Mass: 24522.346 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-215 (FAB FRAGMENT, HEAVY CHAIN) / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Antibody ANTIBODY


Mass: 23218.730 Da / Num. of mol.: 2 / Fragment: RESIDUES 3-214 (FAB FRAGMENT, LIGHT CHAIN) / Source method: isolated from a natural source / Details: HYBRIDOMA / Source: (natural) MUS MUSCULUS (house mouse) / References: UniProt: P01837*PLUS
#4: Protein/peptide CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2


Mass: 1512.706 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-28 / Source method: obtained synthetically
Details: RAISED AGAINST THE P1.2 SEROSUBTYPE ANTIGEN SEQUENCE FROM THE PORA PROTEIN FROM NEISSERI MENINGITIDIS
Source: (synth.) NEISSERIA MENINGITIDIS (bacteria) / References: UniProt: Q51220, UniProt: Q9JPT2*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55.78 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 50717 / % possible obs: 87 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8 / % possible all: 45

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QKZ

1qkz


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU ML: 0.19 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2782 5 %RANDOM
Rwork0.223 ---
obs0.225 53115 87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.41 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å20 Å20 Å2
2---2.14 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7725 0 0 395 8120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0217926
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9410785
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025960
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.22965
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.54980
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02828067
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64832946
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5384.52718
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

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L1616tight positional0.060.05
2H2492tight positional0.070.05
3A440tight positional0.110.05
1L1616tight thermal0.130.5
2H2492tight thermal0.110.5
3A440tight thermal0.170.5
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.407 107
Rwork0.313 1991
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)
13.1078-3.83534.12737.063-3.49439.38170.27040.0861-0.453-0.356-0.12040.51251.6278-0.2052-0.150.4077-0.02070.02230.2104-0.06320.156530.4412.965-4.401
21.4565-0.40921.41832.5482.327511.1804-0.2495-0.08160.22450.0366-0.13620.0918-0.7326-0.62580.38570.17020.1087-0.08230.2086-0.05440.15328.36524.525-2.98
30.9491.2240.63543.86870.52621.22680.0233-0.1126-0.04050.03890.02880.03370.02430-0.0520.0120.03910.00770.12940.0110.119343.13715.03730.601
41.3206-1.2524.02175.3013-0.816210.4880.3153-0.1046-0.00260.6566-0.1890.17672.3444-0.4157-0.12630.9007-0.07580.0590.304-0.06720.153669.20888.867-3.902
52.1746-0.51621.60582.3561.99519.5234-0.345-0.14870.4260.2498-0.2534-0.0446-0.5763-0.56490.59850.27490.0928-0.07940.3108-0.08390.292168.444110.654-3.252
61.50971.03520.39095.28050.31471.1414-0.0409-0.07850.1346-0.37190.02180.45990.0769-0.11740.01910.14260.0432-0.06020.14810.03320.211983.381101.40630.564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L3 - 107
2X-RAY DIFFRACTION2H2 - 122
3X-RAY DIFFRACTION3L108 - 213
4X-RAY DIFFRACTION3H123 - 215
5X-RAY DIFFRACTION3A5 - 62
6X-RAY DIFFRACTION4K3 - 107
7X-RAY DIFFRACTION5M2 - 122
8X-RAY DIFFRACTION6K108 - 213
9X-RAY DIFFRACTION6M123 - 215
10X-RAY DIFFRACTION6B5 - 62

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