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- PDB-1m1j: Crystal structure of native chicken fibrinogen with two different... -

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Basic information

Entry
Database: PDB / ID: 1m1j
TitleCrystal structure of native chicken fibrinogen with two different bound ligands
Components
  • Fibrinogen alpha subunit
  • Fibrinogen beta chain
  • Fibrinogen gamma chain
  • GLY-HIS-ARG-PRO peptide
  • GLY-PRO-ARG-PRO peptide
KeywordsBLOOD CLOTTING / COILED COILS / DISULFIDE RINGS / FIBRINOGEN
Function / homology
Function and homology information


fibrinogen complex / blood coagulation, fibrin clot formation / protein polymerization / cell-matrix adhesion / platelet activation / platelet aggregation / protein-macromolecule adaptor activity / collagen-containing extracellular matrix / signaling receptor binding / extracellular space / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Fibrinogen gamma chain / Fibrinogen alpha chain / Fibrinogen beta chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYang, Z. / Kollman, J.M. / Pandi, L. / Doolittle, R.F.
Citation
Journal: Biochemistry / Year: 2001
Title: Crystal Structure of Native Chicken Fibrinogen at 2.7 A Resolution
Authors: Yang, Z. / Kollman, J.M. / Pandi, L. / Doolittle, R.F.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal Structure of Native Chicken Fibrinogen at 5.5-A Resolution
Authors: Yang, Z. / Mochalkin, I. / Veerapandian, L. / Riley, M. / Doolittle, R.F.
#2: Journal: Nature / Year: 1997
Title: Crystal Sturctures of Fragment D from Human Fibrinogen and its Crosslinked Counterpart from Fibrin
Authors: Spraggon, G. / Everse, S.J. / Doolittle, R.F.
#3: Journal: Biochemistry / Year: 1998
Title: Crystal Structure of Fragment Double-d from Human Fibrin with Two Different Bound Ligands
Authors: Everse, S.J. / Spraggon, G. / Veerapandian, L. / Riley, M. / Doolittle, R.F.
History
DepositionJun 19, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJun 26, 2002ID: 1JFE
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE According to the authors, the published sequence of chicken fibrinogen is incorrect. In ...SEQUENCE According to the authors, the published sequence of chicken fibrinogen is incorrect. In the alpha chain, residue 49 is GLY, not CYS. In the beta chain, residue 1 genetically must be a GLN. In the gamma chain, residue 286 is ALA, not ARG. Chains G and H mimic A16-A19 of the fibrin sequence with PRO replacing ILE A19 of the fibrin sequence. Chains I and J mimic B19-B22 of the fibrin sequence, with GLY replacing ALA B19 of the fibrin sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibrinogen alpha subunit
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
D: Fibrinogen alpha subunit
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
G: GLY-PRO-ARG-PRO peptide
H: GLY-PRO-ARG-PRO peptide
I: GLY-HIS-ARG-PRO peptide
J: GLY-HIS-ARG-PRO peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,77822
Polymers309,84810
Non-polymers1,93012
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.090, 100.020, 200.090
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Fibrinogen alpha subunit


Mass: 54241.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: blood / References: UniProt: P14448
#2: Protein Fibrinogen beta chain /


Mass: 52874.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: blood / References: UniProt: Q02020
#3: Protein Fibrinogen gamma chain /


Mass: 46913.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: blood / References: UniProt: O93568

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Protein/peptide , 2 types, 4 molecules GHIJ

#4: Protein/peptide GLY-PRO-ARG-PRO peptide


Mass: 426.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide is chemically synthesized.
#5: Protein/peptide GLY-HIS-ARG-PRO peptide


Mass: 467.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide is chemically synthesized.

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Sugars , 2 types, 8 molecules

#6: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

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Non-polymers , 1 types, 4 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlprotein1drop
20.15 M1dropNaCl
30.05 Mimidazole1droppH7.0
40.5 MTMAO1reservoir
50.05 MMES1reservoirpH6.0
61 mM1reservoirCaCl2
71 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2000
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 121776 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.1
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.311 / % possible all: 67.8
Reflection
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 20 Å / Num. measured all: 1506048
Reflection shell
*PLUS
% possible obs: 67.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FRAGMENT D FROM STRUCTURE 1FZC

1fzc


Resolution: 2.7→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.256 5863 -RANDOM
Rwork0.227 ---
all0.231 ---
obs-110727 93.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15993 0 124 0 16117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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