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- PDB-1ovo: CRYSTALLOGRAPHIC REFINEMENT OF JAPANESE QUAIL OVOMUCOID, A KAZAL-... -

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Entry
Database: PDB / ID: 1ovo
TitleCRYSTALLOGRAPHIC REFINEMENT OF JAPANESE QUAIL OVOMUCOID, A KAZAL-TYPE INHIBITOR, AND MODEL BUILDING STUDIES OF COMPLEXES WITH SERINE PROTEASES
ComponentsOVOMUCOID THIRD DOMAIN
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: 1.9 Å
AuthorsWeber, E. / Papamokos, E. / Bode, W. / Huber, R. / Kato, I. / Laskowskijunior, M.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Crystallographic refinement of Japanese quail ovomucoid, a Kazal-type inhibitor, and model building studies of complexes with serine proteases.
Authors: Papamokos, E. / Weber, E. / Bode, W. / Huber, R. / Empie, M.W. / Kato, I. / Laskowski Jr., M.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors
Authors: Marquart, M. / Walter, J. / Deisenhofer, J. / Bode, W. / Huber, R.
#2: Journal: J.Mol.Biol. / Year: 1981
Title: Crystallization,Crystal Structure Analysis and Molecular Model of the Third Domain of Japanese Quail Ovomucoid,A Kazal Type Inhibitor
Authors: Weber, E. / Papamokos, E. / Bode, W. / Huber, R. / Kato, I. / Laskowskijunior, M.
History
DepositionJan 18, 1982Processing site: BNL
Revision 1.0May 26, 1982Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OVOMUCOID THIRD DOMAIN
B: OVOMUCOID THIRD DOMAIN
C: OVOMUCOID THIRD DOMAIN
D: OVOMUCOID THIRD DOMAIN


Theoretical massNumber of molelcules
Total (without water)24,2714
Polymers24,2714
Non-polymers00
Water82946
1
A: OVOMUCOID THIRD DOMAIN
B: OVOMUCOID THIRD DOMAIN

A: OVOMUCOID THIRD DOMAIN
B: OVOMUCOID THIRD DOMAIN


Theoretical massNumber of molelcules
Total (without water)24,2714
Polymers24,2714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area5660 Å2
ΔGint-26 kcal/mol
Surface area10670 Å2
MethodPISA, PQS
2
C: OVOMUCOID THIRD DOMAIN

C: OVOMUCOID THIRD DOMAIN

C: OVOMUCOID THIRD DOMAIN

C: OVOMUCOID THIRD DOMAIN


Theoretical massNumber of molelcules
Total (without water)24,2714
Polymers24,2714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
MethodPQS
3
D: OVOMUCOID THIRD DOMAIN

D: OVOMUCOID THIRD DOMAIN

D: OVOMUCOID THIRD DOMAIN

D: OVOMUCOID THIRD DOMAIN


Theoretical massNumber of molelcules
Total (without water)24,2714
Polymers24,2714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.000, 92.000, 64.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Atom site foot note1: SEE REMARK 5. / 2: RESIDUE 12 OF EACH CHAIN IS A CIS-PROLINE.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.3714, -0.5829, -0.7226), (-0.4603, 0.5603, -0.6886), (0.8064, 0.5885, -0.0602)79.05, 63.26, -32.97
2given(0.3847, -0.9228, -0.0174), (-0.9222, -0.3851, 0.0222), (-0.0273, 0.0075, -0.9996)100.13, 147.39, 131.37
DetailsTHE MTRIX RECORDS BELOW DESCRIBE THE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE INDIVIDUAL DOMAINS IN THIS ENTRY. MTRIX 1 RELATES CHAIN A TO CHAIN B BY A PSEUDO-FOUR-FOLD ROTATION. MTRIX 2 RELATES CHAIN C TO CHAIN D BY A PSEUDO-TWO-FOLD ROTATION. SEE REFERENCE 2 ABOVE FOR A COMPLETE DESCRIPTION OF THESE SYMMETRY AXES. THESE MATRICES WERE OBTAINED BY COMPARING THE BACKBONE AND CB ATOMS OF THE MOLECULES. (THE FIRST SIX RESIDUES WERE EXCLUDED FROM THIS CALCULATION.)

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Components

#1: Protein
OVOMUCOID THIRD DOMAIN


Mass: 6067.842 Da / Num. of mol.: 4
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.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MATERIAL USED IS POLYMORPHIC WITH 20 PER CENT GLY 32 AND 80 PER CENT SER 32. IT IS PREMATURE AT ...THE MATERIAL USED IS POLYMORPHIC WITH 20 PER CENT GLY 32 AND 80 PER CENT SER 32. IT IS PREMATURE AT THE PRESENT STAGE OF THE ANALYSIS TO DRAW CONCLUSIONS ABOUT AN ORDERED ARRANGEMENT OF THE VARIANTS IN THE CRYSTAL. THE MAJOR POLYMORPH HAS BEEN ASSIGNED TO THE FOUR DOMAINS IN THIS ENTRY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9.5 / Method: unknown / Details: Weber, E., (1981) J.Mol.Biol., 149, 109.
Components of the solutions
*PLUS
Conc.: 0.96-1.0 M / Common name: citrate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 19537 / % possible obs: 75 % / Num. measured all: 63795 / Rmerge(I) obs: 0.084

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Processing

SoftwareName: REAL-SPACE / Version: REFINEMENT / Classification: refinement
RefinementHighest resolution: 1.9 Å
Details: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 0 46 1730
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 15980 / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS

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