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- PDB-1ggt: THREE-DIMENSIONAL STRUCTURE OF A TRANSGLUTAMINASE: HUMAN BLOOD CO... -

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Basic information

Entry
Database: PDB / ID: 1ggt
TitleTHREE-DIMENSIONAL STRUCTURE OF A TRANSGLUTAMINASE: HUMAN BLOOD COAGULATION FACTOR XIII
ComponentsCOAGULATION FACTOR XIII
KeywordsBLOOD 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 / Resolution: 2.65 Å
AuthorsYee, V.C. / Pedersen, L.C. / Trong, I.L. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C.
Citation
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.
#1: Journal: Protein Sci. / Year: 1994
Title: The Catalytic Triad and Proposed Mechanism of Transglutaminases Based on the Crystal Structure of Factor Xiii
Authors: Pedersen, L.C. / Yee, V.C. / Trong, I.L. / Bishop, P.D. / Teller, D.C. / Stenkamp, R.E.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Human Recombinant Factor Xiii from Saccharomyces Cerevisiae: Crystallization and Preliminary X-Ray Data
Authors: Bishop, P.D. / Lasser, G.W. / Trong, I.L. / 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
DepositionJan 25, 1994Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET SHEET *B1A* FORMS A BETA SANDWICH DOMAIN WITH SHEETS *B2A* AND *B2B*. SHEET *B1B* FORMS A ...SHEET SHEET *B1A* FORMS A BETA SANDWICH DOMAIN WITH SHEETS *B2A* AND *B2B*. SHEET *B1B* FORMS A BETA SANDWICH DOMAIN WITH SHEETS *B2C* AND *B2D*. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, THE BIFURCATED SHEET IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. STRANDS 3, 4, AND 5 OF SHEET *B2A* AND *B2B* ARE IDENTICAL. STRANDS 3, 4, AND 5 OF SHEET *B2C* AND *B2D* ARE IDENTICAL. IN SHEET *B7A* AND *B7B* OF *SHEET* RECORDS BELOW, STRANDS 1 - 3 AND 4 - 7 FORM TWO BETA SHEETS THAT COME TOGETHER TO MAKE A BARREL. IN SHEET *B8A* AND *B8B* OF *SHEET* RECORDS BELOW, STRANDS 1 - 3 AND 4 - 7 FORM TWO BETA SHEETS THAT COME TOGETHER TO MAKE A BARREL.

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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)166,4682
Polymers166,4682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.200, 182.700, 93.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO A 411 / 2: CIS PROLINE - PRO B 411
3: GLU B 578 - PRO B 579 OMEGA = 145.65 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.590321, 0.807168, 0.000528), (0.807132, -0.5903, 0.009151), (0.007699, 0.007699, -0.99996)
Vector: -53.0093, 104.4717, 75.66453)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 8 .. 727 B 8 .. 727 0.815

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Components

#1: Protein COAGULATION FACTOR XIII


Mass: 83233.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD
References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 5.8 / Method: vapor diffusion, hanging drop / Details: Bishop, P.D., (1990) J.Biol.Chem., 23, 13888.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %satammonium sulfate1reservoir0.8M
210 %satammonium sulfate1drop0.4M
320 mMsodium acetate1drop
410 mM2-mercaptoethanol1drop
50.2 %1,2,3-heptanetriol1drop
68.2 mg/mlfactor XIII1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.65→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.216 --
obs0.216 65937 97.6 %
Refinement stepCycle: LAST / Resolution: 2.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11382 0 0 0 11382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.183
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

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