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- PDB-4uv4: Crystal structure of anti-FPR Fpro0165 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 4uv4
TitleCrystal structure of anti-FPR Fpro0165 Fab fragment
Components(FPRO0165 FAB) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY ENGINEERING / PHAGE DISPLAY / LONG CDR / FORMYL PEPTIDE RECEPTOR-1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsDouthwaite, J.A. / Sridharan, S. / Huntington, C. / Marwood, R. / Hammersley, J. / Hakulinen, J.K. / Ek, M. / Sjogren, T. / Rider, D. / Privezentzev, C. ...Douthwaite, J.A. / Sridharan, S. / Huntington, C. / Marwood, R. / Hammersley, J. / Hakulinen, J.K. / Ek, M. / Sjogren, T. / Rider, D. / Privezentzev, C. / Seaman, J.C. / Cariuk, P. / Knights, V. / Young, J. / Wilkinson, T. / Sleeman, M. / Finch, D.K. / Lowe, D.C. / Vaughan, T.J.
CitationJournal: Mabs / Year: 2015
Title: Affinity Maturation of a Novel Antagonistic Human Monoclonal Antibody with a Long Vh Cdr3 Targeting the Class a Gpcr Formyl-Peptide Receptor 1.
Authors: Douthwaite, J.A. / Sridharan, S. / Huntington, C. / Hammersley, J. / Marwood, R. / Hakulinen, J.K. / Ek, M. / Sjogren, T. / Rider, D. / Privezentzev, C. / Seaman, J.C. / Cariuk, P. / ...Authors: Douthwaite, J.A. / Sridharan, S. / Huntington, C. / Hammersley, J. / Marwood, R. / Hakulinen, J.K. / Ek, M. / Sjogren, T. / Rider, D. / Privezentzev, C. / Seaman, J.C. / Cariuk, P. / Knights, V. / Young, J. / Wilkinson, T. / Sleeman, M. / Finch, D.K. / Lowe, D.C. / Vaughan, T.J.
History
DepositionAug 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: FPRO0165 FAB
L: FPRO0165 FAB


Theoretical massNumber of molelcules
Total (without water)49,9542
Polymers49,9542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-22.2 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.350, 128.350, 90.601
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody FPRO0165 FAB


Mass: 26000.039 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 EBNA / Production host: HOMO SAPIENS (human)
#2: Antibody FPRO0165 FAB


Mass: 23953.803 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 EBNA / Production host: HOMO SAPIENS (human)

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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: 4.3 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growDetails: 0.1 M TRIS-HCL PH 7.5-8.0, 18% PEG8000, 0.18-0.2 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.985
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.985 Å / Relative weight: 1
ReflectionResolution: 3.08→30 Å / Num. obs: 4512 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 76.88 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 3.08→3.85 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQK

1aqk


Resolution: 3.08→39.2 Å / Cor.coef. Fo:Fc: 0.8321 / Cor.coef. Fo:Fc free: 0.7915 / SU R Cruickshank DPI: 0.856 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.796 / SU Rfree Blow DPI: 0.385 / SU Rfree Cruickshank DPI: 0.396
Details: REFINEMENT WAS PERFORMED USIN RESOLUTION FAB FRAGMENT STRUCTURES WITH HIGH HOMOLOGY TO FPR0165 FAB WERE USED TO BUILD A MODEL FOR TARGET RESTRAINTS, PDB CODE 3AAZ AND PDB CODE 3GHB FOR THE ...Details: REFINEMENT WAS PERFORMED USIN RESOLUTION FAB FRAGMENT STRUCTURES WITH HIGH HOMOLOGY TO FPR0165 FAB WERE USED TO BUILD A MODEL FOR TARGET RESTRAINTS, PDB CODE 3AAZ AND PDB CODE 3GHB FOR THE LIGHT AND HEAVY CHAINS RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2804 812 5.02 %RANDOM
Rwork0.2427 ---
obs0.2446 16180 99.58 %-
Displacement parametersBiso mean: 111.81 Å2
Baniso -1Baniso -2Baniso -3
1--29.3105 Å20 Å20 Å2
2---29.3105 Å20 Å2
3---58.621 Å2
Refine analyzeLuzzati coordinate error obs: 0.826 Å
Refinement stepCycle: LAST / Resolution: 3.08→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3398 0 0 0 3398
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013485HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.274746HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1140SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes505HARMONIC5
X-RAY DIFFRACTIONt_it3485HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion22.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion452SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3938SEMIHARMONIC4
LS refinement shellResolution: 3.08→3.29 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2765 149 5.26 %
Rwork0.2878 2685 -
all0.2872 2834 -
obs--99.58 %

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