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- PDB-1f13: RECOMBINANT HUMAN CELLULAR COAGULATION FACTOR XIII -

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Basic information

Entry
Database: PDB / ID: 1f13
TitleRECOMBINANT HUMAN CELLULAR COAGULATION FACTOR XIII
ComponentsCELLULAR COAGULATION FACTOR XIII ZYMOGEN
KeywordsCOAGULATION FACTOR / COAGULATION / TRANSGLUTAMINASE / TRANSFERASE / 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 / : ...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 / : / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWeiss, M.S. / Hilgenfeld, R.
Citation
Journal: FEBS Lett. / Year: 1998
Title: Two non-proline cis peptide bonds may be important for factor XIII function.
Authors: Weiss, M.S. / Metzner, H.J. / Hilgenfeld, R.
#1: 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.
#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: FEBS Lett. / Year: 1990
Title: Crystallization of Blood Coagulation Factor Xiii by an Automated Procedure
Authors: Hilgenfeld, R. / Liesum, A. / Storm, R. / Metzner, H.J. / Karges, H.E.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,4682
Polymers166,4682
Non-polymers00
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-15 kcal/mol
Surface area56520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.590, 72.780, 101.050
Angle α, β, γ (deg.)90.00, 106.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.395373, -0.917773, 0.037045), (-0.917811, 0.393162, -0.055189), (0.036086, -0.055821, -0.997788)
Vector: 74.2279, 51.8551, 68.7775)
DetailsTHERE ARE TWO CHAINS IN THE ASYMMETRIC UNIT WITH CHAIN IDENTIFIERS A AND B. DISORDERED REGIONS INCLUDE RESIDUES 1 - 4, 37 - 38, 729 - 731 OF CHAIN A AND RESIDUES 1 - 5, 37 - 40, 729 - 731 OF CHAIN B. POORLY ORDERED REGIONS ARE RESIDUES 5 - 6 OF CHAIN A AND 6 OF CHAIN B, RESIDUES 35 - 36, 39, 510 - 516 OF CHAIN A AND 35 - 36, AND 510 - 516 OF CHAIN B.

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Components

#1: Protein CELLULAR COAGULATION FACTOR XIII ZYMOGEN / CFXIII


Mass: 83233.922 Da / Num. of mol.: 2 / Fragment: A2-HOMODIMER
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.: 487 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.1 %
Crystal growpH: 6.2
Details: THE PROTEIN WAS CRYSTALLIZED FROM 1-2% PEG 6000, 100 MM MES, PH 6.2-6.4
PH range: 6.2-6.4
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.4 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-4 mg/mlprotein1drop
2100 mMMES1reservoir
31-2 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.912
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 5, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 89672 / % possible obs: 81.6 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 40.2
Reflection
*PLUS
Num. measured all: 293385

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GGT

1ggt


Resolution: 2.1→40 Å / Data cutoff high absF: 10000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R / σ(F): 0 / Details: BULK SOLVENT MODEL INCLUDED
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1796 2 %RANDOM
Rwork0.183 ---
obs0.183 89649 82 %-
Displacement parametersBiso mean: 39.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 40 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11556 0 0 487 12043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.562
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.336 86 2 %
Rwork0.313 4303 -
obs--40 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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