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Yorodumi- PDB-1ahw: A COMPLEX OF EXTRACELLULAR DOMAIN OF TISSUE FACTOR WITH AN INHIBI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ahw | ||||||
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Title | A COMPLEX OF EXTRACELLULAR DOMAIN OF TISSUE FACTOR WITH AN INHIBITORY FAB (5G9) | ||||||
Components |
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Keywords | COMPLEX (IMMUNOGLOBULIN/TISSUE FACTOR) / BLOOD COAGULATION / TISSUE FACTOR / FAB / COMPLEX / ANTIBODY / COMPLEX (IMMUNOGLOBULIN-TISSUE FACTOR) / COMPLEX (IMMUNOGLOBULIN-TISSUE FACTOR) complex | ||||||
Function / homology | Function and homology information activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / IgG immunoglobulin complex / positive regulation of TOR signaling ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / IgG immunoglobulin complex / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation / B cell differentiation / positive regulation of interleukin-8 production / phospholipid binding / protein processing / cytokine-mediated signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / blood coagulation / collagen-containing extracellular matrix / protease binding / positive regulation of cell migration / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Huang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ahw.cif.gz | 224.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ahw.ent.gz | 186.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ahw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/1ahw ftp://data.pdbj.org/pub/pdb/validation_reports/ah/1ahw | HTTPS FTP |
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-Related structure data
Related structure data | 1fgnSC 1tfhSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (-0.253131, -0.068772, 0.964984), Vector: |
-Components
#1: Antibody | Mass: 23810.203 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN RESIDUES 1 - 214 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: BL21 / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P01837 #2: Antibody | Mass: 23175.799 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN RESIDUES 1 - 214 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: BL21 / Organ: BLOOD / Tissue: BLOOD / References: PIR: S49220, UniProt: X5J519*PLUS #3: Protein | Mass: 24826.512 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HUMAN TISSUE FACTOR EXTRACELLU / Organ: BLOOD / Plasmid: PTRCHISC (INVITROGEN) / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES Gene (production host): HUMAN TISSUE FACTOR EXTRACELLULAR DOMAIN Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13726 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 64 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: TF-5G9 CRYSTAL WERE GROWN IN 1.7-2.0M AMMONIUM SULFATE, 0.1M SODIUM CITRATE, PH 5.0-5.5, 0.2% 2-METHYL-2,4-PENTANE-DIOL (MPD), AND 2% PEG 600 AT AN EQUIMOLAR 5G9:TF RATIO. THE CRYSTALS GREW ...Details: TF-5G9 CRYSTAL WERE GROWN IN 1.7-2.0M AMMONIUM SULFATE, 0.1M SODIUM CITRATE, PH 5.0-5.5, 0.2% 2-METHYL-2,4-PENTANE-DIOL (MPD), AND 2% PEG 600 AT AN EQUIMOLAR 5G9:TF RATIO. THE CRYSTALS GREW EXTREMELY SLOWLY, TAKING 6-9 MONTHS TO REACH A MAXIMAL SIZE OF 0.4 X 0.4 X 0.8 MM3., pH 7.0 PH range: 5.0-5.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / PH range low: 5.5 / PH range high: 5 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→47 Å / Num. obs: 42650 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 42.4 Å2 / Rsym value: 0.135 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3→3.19 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.9 / Rsym value: 0.43 / % possible all: 87 |
Reflection | *PLUS Num. measured all: 118598 / Rmerge(I) obs: 0.135 |
Reflection shell | *PLUS % possible obs: 87 % / Rmerge(I) obs: 0.446 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TISSUE FACTOR (PDB ENTRY 1TFH) AND FAB 5G9 (PDB ENTRY 1FGN) Resolution: 3→7 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 38.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→7 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 3→3.17 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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