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- PDB-9jbq: Structure of the complex between h1F3 Fab and PcrV fragment -

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Basic information

Entry
Database: PDB / ID: 9jbq
TitleStructure of the complex between h1F3 Fab and PcrV fragment
Components
  • Heavy chain
  • PcrV
  • light chain
KeywordsANTIMICROBIAL PROTEIN/IMMUNE SYSTEM / Complex / Fab / ANTIMICROBIAL PROTEIN / ANTIMICROBIAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyLow calcium response V antigen / Virulence-associated V antigen superfamily / V antigen (LcrV) protein / extracellular region / PcrV
Function and homology information
Biological speciesHomo sapiens (human)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNumata, S. / Hara, T. / Izawa, M. / Okuno, Y. / Sato, Y. / Yamane, S. / Maki, H. / Sato, T. / Yamano, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Antimicrob.Agents Chemother. / Year: 2024
Title: Novel humanized anti-PcrV monoclonal antibody COT-143 protects mice from lethal Pseudomonas aeruginosa infection via inhibition of toxin translocation by the type III secretion system.
Authors: Numata, S. / Hara, T. / Izawa, M. / Okuno, Y. / Sato, Y. / Yamane, S. / Maki, H. / Sato, T. / Yamano, Y.
History
DepositionAug 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heavy chain
B: light chain
C: PcrV


Theoretical massNumber of molelcules
Total (without water)62,6473
Polymers62,6473
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-28 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.680, 52.005, 69.964
Angle α, β, γ (deg.)99.02, 104.61, 115.21
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Heavy chain


Mass: 24621.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody light chain


Mass: 23446.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein PcrV / Virulence-associated V antigen


Mass: 14579.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pcrV, lcrV, CAZ10_30180, NCTC13621_01744, PAERUG_P19_London_7_VIM_2_05_10_06389
Production host: Escherichia coli (E. coli) / References: UniProt: O30527
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.125 M Calcium chloride dehydrate, 0.1 M Sodium acetate trihydrate pH5.6, 24%w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 13, 2013
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33570 / % possible obs: 94.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.074 / Χ2: 1.404 / Net I/σ(I): 11 / Num. measured all: 125724
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.033.70.32215790.843190.9
2.03-2.073.70.31216470.909193
2.07-2.113.80.26116070.929192
2.11-2.153.70.24516451.009192.4
2.15-2.23.70.21316561.064193.5
2.2-2.253.70.19516631.047192.9
2.25-2.313.70.17816391.119194.2
2.31-2.373.70.1616741.127193.6
2.37-2.443.70.15916651.224194.4
2.44-2.523.70.1416601.27194.4
2.52-2.613.70.12417181.303195
2.61-2.713.80.11316631.399195.3
2.71-2.843.80.09716751.496195.4
2.84-2.993.80.08716991.693195.7
2.99-3.173.80.07617471.735196.6
3.17-3.423.80.06317021.874196.8
3.42-3.763.80.05317152.098197.4
3.76-4.313.80.04617422.074197.8
4.31-5.433.80.0417351.971198.5
5.43-103.70.03417391.675198.1

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 2→23.499 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 1697 5.06 %
Rwork0.1694 --
obs0.1718 33563 94.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→23.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 0 309 4570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074361
X-RAY DIFFRACTIONf_angle_d1.1365927
X-RAY DIFFRACTIONf_dihedral_angle_d13.8791562
X-RAY DIFFRACTIONf_chiral_restr0.075673
X-RAY DIFFRACTIONf_plane_restr0.005754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05850.26581490.192413X-RAY DIFFRACTION88
2.0585-2.12490.25871310.18072606X-RAY DIFFRACTION92
2.1249-2.20080.24181310.18252615X-RAY DIFFRACTION94
2.2008-2.28890.22561530.18112607X-RAY DIFFRACTION93
2.2889-2.39290.26871290.18012639X-RAY DIFFRACTION94
2.3929-2.5190.24361220.19012671X-RAY DIFFRACTION94
2.519-2.67660.25911450.18552688X-RAY DIFFRACTION95
2.6766-2.88290.23581510.18212684X-RAY DIFFRACTION95
2.8829-3.17240.20541550.17672704X-RAY DIFFRACTION96
3.1724-3.630.19281500.15972692X-RAY DIFFRACTION97
3.63-4.56790.19041380.14532759X-RAY DIFFRACTION98
4.5679-100.18341430.16192788X-RAY DIFFRACTION99

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