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- PDB-1ex0: HUMAN FACTOR XIII, MUTANT W279F ZYMOGEN -

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Basic information

Entry
Database: PDB / ID: 1ex0
TitleHUMAN FACTOR XIII, MUTANT W279F ZYMOGEN
ComponentsCOAGULATION FACTOR XIII A CHAIN
KeywordsTRANSFERASE / TRANSGLUTAMINASE / BLOOD COAGULATION / mutant / W279F / oxyanion
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 / blood microparticle / Interleukin-4 and Interleukin-13 signaling / 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 / Transglutaminases active site. ...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 / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / PHOSPHATE ION / Coagulation factor XIII A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsGarzon, R.J. / Pratt, K.P. / Bishop, P.D. / Le Trong, I. / Stenkamp, R.E. / Teller, D.C.
Citation
Journal: To be Published
Title: Tryptophan 279 is Essential for the Transglutaminase Activity of Coagulation Factor XIII: Functional and Structural Characterization
Authors: Garzon, R.J. / Pratt, K.P. / Bishop, P.D. / Le Trong, I. / Stenkamp, R.E. / Teller, D.C.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Identification of the Calcium Binding Site and a Novel Ytterbium Site in Blood Coagulation Factor XIII by X-Ray Crystallography
Authors: Fox, B.A. / Yee, V.C. / Pedersen, L.C. / Le Trong, I. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C.
History
DepositionApr 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 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: COAGULATION FACTOR XIII A CHAIN
B: COAGULATION FACTOR XIII A CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,44813
Polymers166,6262
Non-polymers82211
Water23,5281306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-39 kcal/mol
Surface area54930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.540, 70.640, 133.380
Angle α, β, γ (deg.)90.00, 106.08, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is the dimer composed of chains A of subunit 1 and chains B of subunit 2. A non-crystallographic twofold axis relates the two dimers.

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Components

#1: Protein COAGULATION FACTOR XIII A CHAIN


Mass: 83312.984 Da / Num. of mol.: 2 / Mutation: W279F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue fraction: PLASMA, PLATELET, PLACENTA / Plasmid: PD16 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ZM118
References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1306 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 - 12 % 1,2-propanediol, 0.1 M Na-K phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.79→28.51 Å / Num. obs: 158697 / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.4
Reflection shellResolution: 1.79→1.84 Å / Rmerge(I) obs: 0.402 / Num. unique all: 8534

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACV 3.5refinement
RefinementResolution: 2→19.94 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1349556.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD, ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.234 5793 4.9 %RANDOM
Rwork0.187 ---
obs-117421 96.6 %-
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å22.38 Å2
2--3.28 Å20 Å2
3----0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11417 0 47 1306 12770
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_deg2.5
X-RAY DIFFRACTIONp_bond_d0.0131.5
X-RAY DIFFRACTIONc_torsion_deg27.22
X-RAY DIFFRACTIONc_torsion_impr_deg2.342
X-RAY DIFFRACTIONp_mcbond_it2.581.5
X-RAY DIFFRACTIONp_mcangle_it3.262
X-RAY DIFFRACTIONp_scbond_it2.572
X-RAY DIFFRACTIONp_scangle_it3.282.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 971 5.1 %
Rwork0.217 18243 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PRP.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5cis_pep279.param

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