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- PDB-4ovo: REFINED X-RAY CRYSTAL STRUCTURES OF THE REACTIVE SITE MODIFIED OV... -

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Basic information

Entry
Database: PDB / ID: 4ovo
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 space
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 ...: / 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 speciesLophura nycthemera (Silver pheasant)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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: Derived calculations / 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 13, 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

Downloads & links

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Assembly

Deposited unit
A: OVOMUCOID THIRD DOMAIN CLEAVED RDI


Theoretical massNumber of molelcules
Total (without water)6,0451
Polymers6,0451
Non-polymers00
Water45025
1
A: OVOMUCOID THIRD DOMAIN CLEAVED RDI

A: OVOMUCOID THIRD DOMAIN CLEAVED RDI


Theoretical massNumber of molelcules
Total (without water)12,0902
Polymers12,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
MethodPQS
2
A: OVOMUCOID THIRD DOMAIN CLEAVED RDI

A: OVOMUCOID THIRD DOMAIN CLEAVED RDI

A: OVOMUCOID THIRD DOMAIN CLEAVED RDI

A: OVOMUCOID THIRD DOMAIN CLEAVED RDI


Theoretical massNumber of molelcules
Total (without water)24,1794
Polymers24,1794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area5650 Å2
ΔGint-31 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.600, 56.600, 76.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Atom site foot note1: RESIDUE PRO 12 IS A CIS PROLINE.
2: THE PEPTIDE BOND BETWEEN MET 18 AND GLU 19 HAS BEEN HYDROLYZED.

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Components

#1: Protein OVOMUCOID THIRD DOMAIN CLEAVED RDI


Mass: 6044.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lophura nycthemera (Silver pheasant) / References: UniProt: P67954
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDE BOND BETWEEN MET 18 AND GLU 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.45 Mammonium sulfate1reservoir
215 mg/mlprotein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 1947 / % possible obs: 82 % / Num. measured all: 5813 / Rmerge(I) obs: 0.0937

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.185 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms418 0 0 25 443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
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_deg2.32
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: 1741 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.7 Å2

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