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- PDB-1qkz: Fab fragment (MN14C11.6) in complex with a peptide antigen derive... -

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Basic information

Entry
Database: PDB / ID: 1qkz
TitleFab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria meningitidis P1.7 serosubtype antigen and domain II from Streptococcal protein G
Components
  • (ANTIBODY) x 2
  • MAJOR OUTER MEMBRANE PROTEIN P1.16
  • PROTEIN G-PRIME
KeywordsIMMUNE SYSTEM / FAB / PORA / NEISSERIA MENINGITIDIS / PORIN
Function / homology
Function and homology information


IgG binding / porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport / extracellular region
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 / : / Ubiquitin-like (UB roll) - #10 / IgG-binding B / B domain ...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 / : / Ubiquitin-like (UB roll) - #10 / IgG-binding B / B domain / 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) / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / Immunoglobulin G-binding protein G / Major outer membrane protein P.IA / Class I subtype P1.16 protein / Protein G'
Similarity search - Component
Biological speciesSTREPTOCOCCUS SP. (bacteria)
MUS MUSCULUS (house mouse)
NEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDerrick, J.P. / Feavers, I. / Maiden, M.C.J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure of an Fab Fragment in Complex with a Meningococcal Serosubtype Antigen and a Protein G Domain
Authors: Derrick, J.P. / Feavers, I.M. / Maiden, M.C.J.
History
DepositionAug 17, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN G-PRIME
H: ANTIBODY
L: ANTIBODY
P: MAJOR OUTER MEMBRANE PROTEIN P1.16


Theoretical massNumber of molelcules
Total (without water)55,6124
Polymers55,6124
Non-polymers00
Water9,476526
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-47.4 kcal/mol
Surface area27460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)43.482, 63.099, 89.374
Angle α, β, γ (deg.)90.00, 81.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN G-PRIME


Mass: 7012.762 Da / Num. of mol.: 1 / Fragment: DOMAIN II / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS SP. (bacteria) / Strain: GROUP G / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q54181, UniProt: P19909*PLUS
#2: Antibody ANTIBODY


Mass: 23755.592 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: HYBRIDOMA / Cell line: MN14C11.6 MURINE HYBRIDOMA / References: EMBL: J245477
#3: Antibody ANTIBODY


Mass: 23954.559 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: HYBRIDOMA / Cell line: MN14C11.6 MURINE HYBRIDOMA / References: EMBL: AJ245476
#4: Protein/peptide MAJOR OUTER MEMBRANE PROTEIN P1.16


Mass: 888.946 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-13 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria) / References: UniProt: Q06140, UniProt: P57041*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FAB ANTIBODY STUDIED HERE IS RELATED IN SEQUENCE TO THE SEQUENCES: CHAIN H TO SWS AAD40243 78 ...THE FAB ANTIBODY STUDIED HERE IS RELATED IN SEQUENCE TO THE SEQUENCES: CHAIN H TO SWS AAD40243 78 PERCENT IDENTITY GAMMA1 HEAVY CHAIN OF MAB7 MUS MUSCULUS CHAIN L TO SWS AAD40242 74 PERCENT IDENTITY KAPPA LIGHT CHAIN OF MAB7 MUS MUSCULUS THE RESIDUE NUMBERING SCHEME USED HERE IS THE KABAT NUMBERING

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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: 2.76 Å3/Da / Density % sol: 43.6 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlFab1drop
28.1 mg/mlprotein G1drop
32.2 mg/mlpeptide1drop
450 mMsodium acetate1reservoir
524 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 34633 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.037 / Net I/σ(I): 17.2
Reflection shellResolution: 1.95→2.04 Å / Rsym value: 0.125 / % possible all: 96
Reflection
*PLUS
Num. measured all: 180259 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.125

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGC

1igc


Resolution: 1.95→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.262 -5 %RANDOM
Rwork0.205 ---
obs0.209 36162 99 %-
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 0 526 4369
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0213
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 32841 / Num. reflection Rfree: 1745
Solvent computation
*PLUS
Displacement parameters
*PLUS

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