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- PDB-1fgn: MONOCLONAL MURINE ANTIBODY 5G9-ANTI-HUMAN TISSUE FACTOR -

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Basic information

Entry
Database: PDB / ID: 1fgn
TitleMONOCLONAL MURINE ANTIBODY 5G9-ANTI-HUMAN TISSUE FACTOR
Components(IMMUNOGLOBULIN FAB 5G9) x 2
KeywordsIMMUNOGLOBULIN / ANTIBODY / FAB / ANTI-TF / MONOCLONAL / MURINE
Function / homology
Function and homology information


alpha-beta T cell receptor complex / IgG immunoglobulin complex / B cell differentiation / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF.5G9 complex.
Authors: Huang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A.
History
DepositionApr 10, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN FAB 5G9
H: IMMUNOGLOBULIN FAB 5G9


Theoretical massNumber of molelcules
Total (without water)46,9862
Polymers46,9862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-28 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.600, 93.700, 60.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IMMUNOGLOBULIN FAB 5G9 / FAB / FAB LIGHT CHAIN / FAB HEAVY CHAIN


Mass: 23810.203 Da / Num. of mol.: 1
Fragment: LIGHT CHAIN RESIDUES 1 - 214, HEAVY CHAIN RESIDUES 1 - 214
Source method: isolated from a natural source / Details: A MONOCLONAL FAB AGAINST HUMAN TISSUE FACTOR / Source: (natural) Mus musculus (house mouse) / Organ: BLOOD / Tissue: BLOOD / References: GenBank: 1613779, UniProt: P01837*PLUS
#2: Antibody IMMUNOGLOBULIN FAB 5G9 / FAB / FAB LIGHT CHAIN / FAB HEAVY CHAIN


Mass: 23175.799 Da / Num. of mol.: 1
Fragment: LIGHT CHAIN RESIDUES 1 - 214, HEAVY CHAIN RESIDUES 1 - 214
Source method: isolated from a natural source / Details: A MONOCLONAL FAB AGAINST HUMAN TISSUE FACTOR / Source: (natural) Mus musculus (house mouse) / Organ: BLOOD / Tissue: BLOOD / References: PIR: S49220
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 46 %
Crystal growpH: 7
Details: TWO SLIGHTLY DIFFERENT CRYSTAL FORMS OF FAB 5G9 WERE OBTAINED USING 17.5% PEG 10K AT PH 8.5 AND 1.35M SODIUM CITRATE AT PH 5.5 AS PRECIPITANTS. THE TWO CRYSTAL FORMS ARE BOTH ORTHORHOMBIC, ...Details: TWO SLIGHTLY DIFFERENT CRYSTAL FORMS OF FAB 5G9 WERE OBTAINED USING 17.5% PEG 10K AT PH 8.5 AND 1.35M SODIUM CITRATE AT PH 5.5 AS PRECIPITANTS. THE TWO CRYSTAL FORMS ARE BOTH ORTHORHOMBIC, P212121, WITH TYPICAL SIZES OF 0.5 X 0.4 X 0.3 MM3 (CITRATE FORM) AND 0.6 X 0.35 X 0.2 MM3 (PEG FORM), WITH SLIGHTLY DIFFERENT CELL PARAMETERS OF A=89.1A, B=90.5A, C=59.3A (CITRATE) AND A=91.6A, B=93.7A, C=60.7A (PEG). PEG FORM IS USED FOR STRUCTURE DETERMINATION., pH 7.0
Crystal grow
*PLUS
pH: 8.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117.5 %PEG1000011
216 mg/mlprotein11

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1992 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→37 Å / Num. obs: 19394 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.075 / Net I/σ(I): 20
Reflection shellResolution: 2.39→2.54 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4 / Rsym value: 0.183 / % possible all: 58.5
Reflection
*PLUS
Num. measured all: 86379 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 58.5 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FABS: HYHEL5-5 AND MCPC603

Resolution: 2.5→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1643 9.9 %RANDOM
Rwork0.217 ---
obs0.217 16666 92.4 %-
Displacement parametersBiso mean: 10.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 0 0 3305
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.281.5
X-RAY DIFFRACTIONx_mcangle_it6.912
X-RAY DIFFRACTIONx_scbond_it6.832
X-RAY DIFFRACTIONx_scangle_it10.322.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.406 169 9.9 %
Rwork0.304 1541 -
obs--73.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.67

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