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- PDB-3ovo: REFINED X-RAY CRYSTAL STRUCTURES OF THE REACTIVE SITE MODIFIED OV... -

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Basic information

Entry
Database: PDB / ID: 3ovo
TitleREFINED X-RAY CRYSTAL STRUCTURES OF THE REACTIVE SITE MODIFIED OVOMUCOID INHIBITOR THIRD DOMAINS FROM SILVER PHEASANT (OMSVP3(ASTERISK)) AND FROM JAPANESE QUAIL (OMJPQ3(ASTERISK))
ComponentsOVOMUCOID THIRD DOMAIN CLEAVED RDI
KeywordsPROTEINASE INHIBITOR (KAZAL)
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCoturnix japonica (Japanese quail)
MethodX-RAY DIFFRACTION / Resolution: 1.55 Å
AuthorsMusil, D. / Bode, W.
CitationJournal: J.Mol.Biol. / Year: 1991
Title: Refined X-ray crystal structures of the reactive site modified ovomucoid inhibitor third domains from silver pheasant (OMSVP3*) and from Japanese quail (OMJPQ3*).
Authors: Musil, D. / Bode, W. / Huber, R. / Laskowski Jr., M. / Lin, T.Y. / Ardelt, W.
History
DepositionMay 13, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OVOMUCOID THIRD DOMAIN CLEAVED RDI


Theoretical massNumber of molelcules
Total (without water)6,0681
Polymers6,0681
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.550, 21.190, 28.140
Angle α, β, γ (deg.)62.09, 115.46, 112.95
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUE PRO 12 IS A CIS PROLINE.
2: THE PEPTIDE BOND BETWEEN LYS 18 AND ASP 19 HAS BEEN HYDROLYZED.

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Components

#1: Protein OVOMUCOID THIRD DOMAIN CLEAVED RDI


Mass: 6067.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coturnix japonica (Japanese quail) / References: UniProt: P01003
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDE BOND BETWEEN LYS 18 AND ASP 19 HAS BEEN HYDROLYZED
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.44 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
22.4 Mammonium sulfate1reservior

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Data collection

Reflection
*PLUS
Highest resolution: 1.55 Å / Num. obs: 5713 / % possible obs: 88.9 % / Num. measured all: 16719 / Rmerge(I) obs: 0.0962

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.192 / Highest resolution: 1.55 Å
Refinement stepCycle: LAST / Highest resolution: 1.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 0 34 455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.022
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3.062
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 5239 / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.7 Å2

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