[English] 日本語
Yorodumi
- PDB-1deq: THE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1deq
TitleTHE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTROM RESOLUTION)
Components
  • FIBRINOGEN
  • FIBRINOGEN (ALPHA CHAIN)
  • FIBRINOGEN (BETA CHAIN)
  • FIBRINOGEN (GAMMA CHAIN)
KeywordsBLOOD CLOTTING / COILED-COIL
Function / homology
Function and homology information


blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / protein polymerization / fibrinolysis / cell-matrix adhesion / platelet aggregation / protein-macromolecule adaptor activity / : ...blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / protein polymerization / fibrinolysis / cell-matrix adhesion / platelet aggregation / protein-macromolecule adaptor activity / : / adaptive immune response / signaling receptor binding / innate immune response / extracellular space / metal ion binding
Similarity search - Function
Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain ...Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Fibrinogen alpha chain / Fibrinogen beta chain / Fibrinogen gamma-B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement (using human fragment d coordinates) / Resolution: 3.5 Å
AuthorsBrown, J.H. / Volkmann, N. / Jun, G. / Henschen-Edman, A.H. / Cohen, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The crystal structure of modified bovine fibrinogen.
Authors: Brown, J.H. / Volkmann, N. / Jun, G. / Henschen-Edman, A.H. / Cohen, C.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Fibrinogen Structure in Projection at 18 Angstroms Resolution
Authors: Rao, S.P.S. / Poojary, M.D. / Elliott Jr., B.W. / Melanson, L.A. / Oriel, B. / Cohen, C.
#2: Journal: J.Mol.Biol. / Year: 1978
Title: Crystals of Modified Fibrinogen: Size, Shape and Packing of Molecules
Authors: Weisel, J.W. / Warren, S.G. / Cohen, C.
#3: Journal: J.Mol.Biol. / Year: 1977
Title: Crystalline States of a Modified Fibrinogen
Authors: Tooney, N.M. / Cohen, C.
History
DepositionNov 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FIBRINOGEN (ALPHA CHAIN)
B: FIBRINOGEN (BETA CHAIN)
C: FIBRINOGEN (GAMMA CHAIN)
D: FIBRINOGEN (ALPHA CHAIN)
E: FIBRINOGEN (BETA CHAIN)
F: FIBRINOGEN (GAMMA CHAIN)
M: FIBRINOGEN
N: FIBRINOGEN (ALPHA CHAIN)
O: FIBRINOGEN (BETA CHAIN)
P: FIBRINOGEN (GAMMA CHAIN)
Q: FIBRINOGEN (ALPHA CHAIN)
R: FIBRINOGEN (BETA CHAIN)
S: FIBRINOGEN (GAMMA CHAIN)
Z: FIBRINOGEN


Theoretical massNumber of molelcules
Total (without water)560,53814
Polymers560,53814
Non-polymers00
Water00
1
A: FIBRINOGEN (ALPHA CHAIN)
B: FIBRINOGEN (BETA CHAIN)
C: FIBRINOGEN (GAMMA CHAIN)
D: FIBRINOGEN (ALPHA CHAIN)
E: FIBRINOGEN (BETA CHAIN)
F: FIBRINOGEN (GAMMA CHAIN)
M: FIBRINOGEN


Theoretical massNumber of molelcules
Total (without water)280,2697
Polymers280,2697
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: FIBRINOGEN (ALPHA CHAIN)
O: FIBRINOGEN (BETA CHAIN)
P: FIBRINOGEN (GAMMA CHAIN)
Q: FIBRINOGEN (ALPHA CHAIN)
R: FIBRINOGEN (BETA CHAIN)
S: FIBRINOGEN (GAMMA CHAIN)
Z: FIBRINOGEN


Theoretical massNumber of molelcules
Total (without water)280,2697
Polymers280,2697
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.006, 94.935, 209.805
Angle α, β, γ (deg.)90.00, 94.41, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAn ~ 4 Angstrom structure of the 285 kDa major fragment of bovine fibrinogen. The alpha-carbon coordinates for both molecules per asymmetric unit are provided. The molecule is a dimer of a heterotrimer. Coordinates with chain ids ABC:DEF and NOP:QRS are the two crystallographically independent dimers. A,D,N, and Q correspond to the A-alpha chain. B,E,O, and R correspond to the B-beta chain. C,F,P, and S correspond to the gamma chain. These alpha-carbon coordinates include the end gamma and beta domains (i.e. the C-terminal globular domains of the gamma and B-beta chains, respectively) and the coiled coils (which are made of the A-alpha, B-beta, and gamma chains.). The density corresponding to the central disulfide knot region is too irregular to be traced at this resolution, and only some coordinates for part of this domain are included where density is seen (designated M and Z for the for the two molecules per a.u.).

-
Components

#1: Protein
FIBRINOGEN (ALPHA CHAIN) / Coordinate model: Cα atoms only


Mass: 42767.410 Da / Num. of mol.: 4 / Fragment: PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02672
#2: Protein
FIBRINOGEN (BETA CHAIN) / Coordinate model: Cα atoms only


Mass: 46901.641 Da / Num. of mol.: 4 / Fragment: PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02676
#3: Protein
FIBRINOGEN (GAMMA CHAIN) / Coordinate model: Cα atoms only


Mass: 46626.605 Da / Num. of mol.: 4 / Fragment: PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P12799
#4: Protein FIBRINOGEN / Coordinate model: Cα atoms only


Mass: 7677.455 Da / Num. of mol.: 2 / Fragment: PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT / Source method: isolated from a natural source / Details: DISORDERED DISULFIDE KNOT REGION / Source: (natural) Bos taurus (domestic cattle)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 277 K / pH: 6.2
Details: 10 mM MES, 5mM sodium azide, 2mM calcium chloride , pH 6.2, temperature 277K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.6 mg/mlprotein11
210 mMMES11
35 mM11NaN3
42 mM11CaCl2

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X12C11.15
SYNCHROTRONNSLS X12C21.15
SYNCHROTRONCHESS F130.908
Detector
TypeIDDetectorDate
BRANDEIS1CCDOct 21, 1996
MARRESEARCH2IMAGE PLATEApr 30, 1996
PRINCETON 2K3CCDNov 23, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.151
20.9081
ReflectionResolution: 3.4→210 Å / Num. all: 79465 / Num. obs: 79465 / % possible obs: 78.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.42 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.05
Reflection shellResolution: 3.38→3.57 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Num. unique all: 6830 / % possible all: 46.7
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 46.7 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: molecular replacement (using human fragment d coordinates)
Starting model: human fragment d coordinates (see related entry 1fza)

1fza


Resolution: 3.5→10 Å / σ(F): 0 / Stereochemistry target values: modified CHARMM in X-Plor
Details: Side chains were included in refinement. At this resolution, however, the correct side chain conformations cannot be generally determined, and only alpha Carbons are deposited here. A B- ...Details: Side chains were included in refinement. At this resolution, however, the correct side chain conformations cannot be generally determined, and only alpha Carbons are deposited here. A B-factor equal to 999 identifies a residue whose density is generally relatively disordered and thus is not included in refinement (but generally positioned using information from non- crystallographically-related copies). Note that of the asymmetric unit's four half-dimers, that designated by chain ids N, O, and P has the most residues included in the refinement, and its electron density is best ordered. The central disulphide knot region could not be traced, and only some coordinates for part of this domain are included (resname=UNK, chainid M and Z for the two molecules per a.u.). Due to anisotropy in the the diffraction, the data in the highest shells (esp. 4.0-3.5) are quite incomplete, and hence the structure is judged overall to at ~4.0 angstroms resolution.
RfactorNum. reflection% reflectionSelection details
Rfree0.37 3444 -random
Rwork0.257 ---
all0.263 69051 --
obs0.263 69051 86.9 %-
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 0 0 3900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.83
X-RAY DIFFRACTIONx_dihedral_angle_d28.1
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1

+
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://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