[English] 日本語
Yorodumi
- PDB-1f13: RECOMBINANT HUMAN CELLULAR COAGULATION FACTOR XIII -

+
Open data


ID or keywords:

Loading...

-
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 / Interleukin-4 and Interleukin-13 signaling ...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 / collagen-containing extracellular matrix / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more