[English] 日本語
Yorodumi
- PDB-4m7h: Crystal structure of tetrameric fibrinogen-like recognition domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m7h
TitleCrystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1
ComponentsFibrinogen C domain-containing protein 1
KeywordsSUGAR BINDING PROTEIN / fibrinogen-like domain / N-acetyl-binding protein / Putative chitin receptor / carbohydrate/sugar binding
Function / homology
Function and homology information


chitin binding / collagen-containing extracellular matrix / extracellular space / membrane / metal ion binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Fibrinogen C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsShrive, A.K. / Greenhough, T.J. / Holmskov, U.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of the Tetrameric Fibrinogen-like Recognition Domain of Fibrinogen C Domain Containing 1 (FIBCD1) Protein.
Authors: Shrive, A.K. / Moeller, J.B. / Burns, I. / Paterson, J.M. / Shaw, A.J. / Schlosser, A. / Sorensen, G.L. / Greenhough, T.J. / Holmskov, U.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibrinogen C domain-containing protein 1
B: Fibrinogen C domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,11810
Polymers51,3762
Non-polymers7428
Water5,350297
1
A: Fibrinogen C domain-containing protein 1
hetero molecules

A: Fibrinogen C domain-containing protein 1
hetero molecules

A: Fibrinogen C domain-containing protein 1
hetero molecules

A: Fibrinogen C domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,80624
Polymers102,7524
Non-polymers2,05420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
2
B: Fibrinogen C domain-containing protein 1
hetero molecules

B: Fibrinogen C domain-containing protein 1
hetero molecules

B: Fibrinogen C domain-containing protein 1
hetero molecules

B: Fibrinogen C domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,66516
Polymers102,7524
Non-polymers91312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)118.560, 118.560, 44.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Fibrinogen C domain-containing protein 1


Mass: 25688.055 Da / Num. of mol.: 2
Fragment: FIBCD1 fibrinogen related domain (UNP residues 236-461)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIBCD1, UNQ701/PRO1346 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N539
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 304 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M Ammonium sulphate, 10% Dioxane, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Sep 30, 2006
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→41.917 Å / Num. all: 41125 / Num. obs: 41125 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.112.80.2142.91615356720.21493.3
2.11-2.2430.16241688655460.16296.6
2.24-2.3930.1342.91609153030.13497.8
2.39-2.583.10.1095.81523949700.10998.3
2.58-2.833.10.0867.21444946010.08698.8
2.83-3.163.30.0698.81407842240.06999.5
3.16-3.653.50.055111298737130.05599.9
3.65-4.473.50.04613.21117531990.04699.9
4.47-6.323.40.04313.3856524960.04399.9
6.32-41.9173.20.04412.9447114010.04499.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.1.4data scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jc9

1jc9


Resolution: 2→41.917 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8908 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 2033 4.8 %random
Rwork0.1827 ---
obs0.1915 41125 97.7 %-
all-41125 --
Solvent computationBsol: 44.0216 Å2
Displacement parametersBiso max: 58.25 Å2 / Biso mean: 21.3129 Å2 / Biso min: 7.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.292 Å20 Å20 Å2
2---1.292 Å20 Å2
3---2.584 Å2
Refinement stepCycle: LAST / Resolution: 2→41.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 41 297 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2441.5
X-RAY DIFFRACTIONc_scbond_it2.0862
X-RAY DIFFRACTIONc_mcangle_it1.8542
X-RAY DIFFRACTIONc_scangle_it3.1062.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 40

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.020.2453490.2241885934
2.02-2.030.2746420.2303865907
2.03-2.050.2271550.2259521007
2.05-2.070.2019430.2029891032
2.07-2.090.2065470.1983921968
2.09-2.110.2323390.2113941980
2.11-2.130.217370.205961998
2.13-2.150.2167410.1883951992
2.15-2.180.1824510.16889551006
2.18-2.20.1939480.17299681016
2.2-2.230.2291420.18719611003
2.23-2.250.2203550.2943998
2.25-2.280.2344530.17889771030
2.28-2.310.2145580.18669651023
2.31-2.340.2277440.1865953997
2.34-2.370.1999600.17939661026
2.37-2.410.1857440.17239921036
2.41-2.440.2358560.18039731029
2.44-2.480.1975530.16629681021
2.48-2.520.1935450.18579731018
2.52-2.560.2171500.18479821032
2.56-2.610.2217490.18219801029
2.61-2.660.2282640.18769791043
2.66-2.710.1877460.17959881034
2.71-2.770.2274560.176310021058
2.77-2.840.2779500.18889641014
2.84-2.910.2203510.177610031054
2.91-2.990.1809450.17159931038
2.99-3.080.2304510.19769811032
3.08-3.170.2228550.18410171072
3.17-3.290.216480.184910131061
3.29-3.420.1991600.17189931053
3.42-3.580.1932560.18499881044
3.58-3.760.2105630.16639901053
3.76-40.1315420.153710381080
4-4.310.1521420.151810071049
4.31-4.740.1415620.153810131075
4.74-5.430.2794650.182110121077
5.43-6.840.2646610.251610121073
6.84-500.010.2356550.21310781133
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4cis_peptide.param
X-RAY DIFFRACTION5other_par4.txt

+
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