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- PDB-1aoc: JAPANESE HORSESHOE CRAB COAGULOGEN -

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Basic information

Entry
Database: PDB / ID: 1aoc
TitleJAPANESE HORSESHOE CRAB COAGULOGEN
ComponentsCOAGULOGEN
KeywordsCOAGULATION FACTOR / CLOTTABLE PROTEIN / CYSTINE KNOT SUPERFAMILY
Function / homology
Function and homology information


hemolymph coagulation / extracellular region
Similarity search - Function
Coagulin / Coagulin / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesTachypleus tridentatus (Chinese horseshoe crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsBergner, A. / Oganessyan, V. / Muta, T. / Iwanaga, S. / Typke, D. / Huber, R. / Bode, W.
CitationJournal: EMBO J. / Year: 1996
Title: Crystal structure of a coagulogen, the clotting protein from horseshoe crab: a structural homologue of nerve growth factor.
Authors: Bergner, A. / Oganessyan, V. / Muta, T. / Iwanaga, S. / Typke, D. / Huber, R. / Bode, W.
History
DepositionNov 28, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COAGULOGEN
B: COAGULOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5793
Polymers39,4832
Non-polymers961
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.200, 52.200, 232.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein COAGULOGEN


Mass: 19741.479 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Tachypleus tridentatus (Chinese horseshoe crab)
References: UniProt: P02681
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47 %
Crystal growpH: 4.5 / Details: 0.5 M AMMONIUM SULFATE, 0.1 M NA-ACETATE, PH 4.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.8-7 mg/mlcoagulogen1drop
20.2 Mammonium sulfate1drop
30.04 Msodium acetate1drop
40.04 mMcadmium sulfate1drop
50.5 Mammonium sulfate1reservoir
60.1 Msodium acetate1reservoir
70.1 mMcadmium sulfate1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 23437 / % possible obs: 95.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.187 / Rsym value: 0.187 / % possible all: 92.3
Reflection shell
*PLUS
% possible obs: 92.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.851model building
X-PLOR3.851refinement
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2→6 Å / Data cutoff high absF: 0.01 / Data cutoff low absF: 100000
Details: THERE ARE SOME REGIONS THAT ARE BAD, IF THEY ARE AT ALL DEFINED IN THE ELECTRON DENSITY, NAMELY THE N-TERMINAL RESIDUES 1 - 6 AND THE REGIONS AROUND THE CLEAVAGE SITES (13 - 23, 42 - 47). ...Details: THERE ARE SOME REGIONS THAT ARE BAD, IF THEY ARE AT ALL DEFINED IN THE ELECTRON DENSITY, NAMELY THE N-TERMINAL RESIDUES 1 - 6 AND THE REGIONS AROUND THE CLEAVAGE SITES (13 - 23, 42 - 47). THE OCCUPANCY OF THESE RESIDUES HAS BEEN SET TO 0.0. THE R VALUE OF THIS MODEL IS 0.195 AND R FREE IS 0.283.
RfactorNum. reflection% reflection
Rfree0.282 2296 10 %
Rwork0.191 --
obs0.191 23067 92 %
Displacement parametersBiso mean: 39.3 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 5 195 2943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.15
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_it1.8
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it1.4
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.341 227 10 %
Rwork0.32 1879 -
obs--92.9 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.32

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