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- PDB-4m7f: Crystal structure of tetrameric fibrinogen-like recognition domai... -

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Basic information

Entry
Database: PDB / ID: 4m7f
TitleCrystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with bound ManNAc
ComponentsFibrinogen C domain-containing protein 1
KeywordsSUGAR BINDING PROTEIN / fibrinogen-like domain / N-acetyl-binding protein
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
2-acetamido-2-deoxy-alpha-D-mannopyranose / Fibrinogen C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Jul 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 1.5Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)52,3129
Polymers51,3762
Non-polymers9367
Water5,783321
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)105,06620
Polymers102,7524
Non-polymers2,31416
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)104,18216
Polymers102,7524
Non-polymers1,42912
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)119.540, 119.540, 44.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

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Protein , 1 types, 2 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

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Sugars , 2 types, 3 molecules

#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
#4: Sugar ChemComp-BM3 / 2-acetamido-2-deoxy-alpha-D-mannopyranose / N-acetyl-alpha-D-mannosamine / 2-acetamido-2-deoxy-alpha-D-mannose / 2-acetamido-2-deoxy-D-mannose / 2-acetamido-2-deoxy-mannose / 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DManpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-mannopyranosamineCOMMON NAMEGMML 1.0
a-D-ManpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 325 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.7M Ammonium sulphate, 7% Dioxane, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9745 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9745 Å / Relative weight: 1
ReflectionResolution: 2.1→53.461 Å / Num. all: 36910 / Num. obs: 36910 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / 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
2.1-2.214.30.1744.22310153610.174100
2.21-2.354.30.1611.62152950380.16199.9
2.35-2.514.30.1262044947540.1299.9
2.51-2.714.30.0947.41914444600.09499.9
2.71-2.974.30.06510.91768941040.06599.8
2.97-3.324.20.05511.71555736850.05599.8
3.32-3.834.10.057.61349232730.0599.7
3.83-4.73.80.05310.21055327920.05399.2
4.7-6.644.30.03814.2939222010.038100
6.64-53.4614.20.03318520412420.03399.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.1.4data scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native FIBCD1 structure

Resolution: 2.1→53.461 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.888 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 1834 5 %random
Rwork0.1869 ---
obs0.1939 36910 99.7 %-
all-36910 --
Solvent computationBsol: 46.3891 Å2
Displacement parametersBiso max: 56.4 Å2 / Biso mean: 18.1329 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.635 Å20 Å20 Å2
2---2.635 Å20 Å2
3---5.271 Å2
Refinement stepCycle: LAST / Resolution: 2.1→53.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 56 321 3908
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2131.5
X-RAY DIFFRACTIONc_scbond_it1.9262
X-RAY DIFFRACTIONc_mcangle_it1.8032
X-RAY DIFFRACTIONc_scangle_it2.7972.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 36

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.120.2783430.2189948991
2.12-2.140.2055580.2031940998
2.14-2.160.2493570.19889791036
2.16-2.180.1788450.17599721017
2.18-2.210.2073460.18489661012
2.21-2.230.2351450.19619891034
2.23-2.260.3064450.23489741019
2.26-2.280.2222450.1953949994
2.28-2.310.2313490.19549911040
2.31-2.340.165330.17279731006
2.34-2.370.2138610.18439471008
2.37-2.40.2041500.18189751025
2.4-2.440.2138520.18369791031
2.44-2.470.2483400.18639711011
2.47-2.510.219590.17689591018
2.51-2.550.2377450.18299851030
2.55-2.60.2246410.19339891030
2.6-2.650.1947600.18579461006
2.65-2.70.2236580.18489531011
2.7-2.750.2241410.19169921033
2.75-2.810.2373660.17739551021
2.81-2.880.2109540.19059621016
2.88-2.950.2691500.19379791029
2.95-3.030.2621530.19549781031
3.03-3.120.2174500.19689641014
3.12-3.220.1923430.19289721015
3.22-3.330.2177590.18439771036
3.33-3.470.2023510.18859901041
3.47-3.620.2008510.17669741025
3.62-3.820.1841540.16599821036
3.82-4.060.1842560.16439731029
4.06-4.370.1883480.15139761024
4.37-4.810.1561650.1689651030
4.81-5.50.2542450.190810151060
5.5-6.930.2546610.24769941055
6.93-500.010.2169550.210810431098
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_parupd.txt

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