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- PDB-1fie: RECOMBINANT HUMAN COAGULATION FACTOR XIII -

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Basic information

Entry
Database: PDB / ID: 1fie
TitleRECOMBINANT HUMAN COAGULATION FACTOR XIII
ComponentsCOAGULATION FACTOR XIII
KeywordsTRANSFERASE / ACYLTRANSFERASE / BLOOD COAGULATION
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / blood microparticle / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / : / Transglutaminase family / Transglutaminase family, C-terminal ig like domain ...Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / : / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Transglutaminase-like superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Coagulation factor XIII A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsYee, V.C. / Teller, D.C.
Citation
Journal: Thromb.Res. / Year: 1995
Title: Structural evidence that the activation peptide is not released upon thrombin cleavage of factor XIII.
Authors: Yee, V.C. / Pedersen, L.C. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C.
#1: Journal: Protein Sci. / Year: 1994
Title: Transglutaminase Factor Xiii Uses Proteinase-Like Catalytic Triad to Crosslink Macromolecules
Authors: Pedersen, L.C. / Yee, V.C. / Bishop, P.D. / Le Trong, I. / Teller, D.C. / Stenkamp, R.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Three-Dimensional Structure of a Transglutaminase: Human Blood Coagulation Factor Xiii
Authors: Yee, V.C. / Pedersen, L.C. / Le Trong, I. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C.
#3: Journal: Biochemistry / Year: 1990
Title: Expression, Purification, and Characterization of Human Factor Xiii in Saccharomyces Cerevisiae
Authors: Bishop, P.D. / Teller, D.C. / Smith, R.A. / Lasser, G.W. / Gilbert, T. / Seale, R.L.
History
DepositionAug 24, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAGULATION FACTOR XIII
B: COAGULATION FACTOR XIII


Theoretical massNumber of molelcules
Total (without water)166,4942
Polymers166,4942
Non-polymers00
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-6 kcal/mol
Surface area54100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.100, 73.130, 134.700
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein COAGULATION FACTOR XIII


Mass: 83246.953 Da / Num. of mol.: 2 / Fragment: A-SUBUNIT (THROMBIN-CLEAVED)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: PLACENTA / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57 %
Crystal growpH: 6 / Details: pH 6.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / PH range low: 6.6 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 %ethanol1reservoir
20.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 50732 / % possible obs: 77.7 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.065
Reflection
*PLUS
Highest resolution: 2.46 Å / Lowest resolution: 9999 Å / Num. measured all: 101939
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.75 Å / % possible obs: 62 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
R-AXISdata scaling
X-PLORphasing
RefinementResolution: 2.5→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.182 --
obs0.182 49681 77 %
Displacement parametersBiso mean: 29.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11372 0 0 557 11929
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.916
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.461
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.461

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