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- PDB-2gkt: Crystal structure of the P14'-Ala32 variant of the N-terminally t... -

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Basic information

Entry
Database: PDB / ID: 2gkt
TitleCrystal structure of the P14'-Ala32 variant of the N-terminally truncated OMTKY3-del(1-5)
ComponentsOvomucoid
KeywordsHYDROLASE INHIBITOR / reactive-site loop / alpha-helix / antiparallel beta-sheet
Function / homology
Function and homology information


molecular function inhibitor activity / 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 ...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 speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsLee, T.W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Insights into the Non-additivity Effects in the Sequence-to-Reactivity Algorithm for Serine Peptidases and their Inhibitors.
Authors: Lee, T.W. / Qasim, M.A. / Laskowski, M. / James, M.N.
History
DepositionApr 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Ovomucoid


Theoretical massNumber of molelcules
Total (without water)5,5991
Polymers5,5991
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.049, 34.692, 25.795
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit of this protein is a monomer which is completely included in each asymmetric unit.

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Components

#1: Protein Ovomucoid


Mass: 5599.314 Da / Num. of mol.: 1 / Fragment: turkey ovomucoid third domain del (1-5) / Mutation: G32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na pH 7.5, 10% v/v isopropanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 23, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.23→40 Å / Num. obs: 11526 / % possible obs: 97.7 %
Reflection shellResolution: 1.23→1.27 Å / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→25.58 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.06 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15067 1131 9.8 %RANDOM
Rwork0.12971 ---
obs0.13183 10393 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.525 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20.05 Å2
2--0.3 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.23→25.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms393 0 0 64 457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022401
X-RAY DIFFRACTIONr_bond_other_d0.0110.02331
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.968546
X-RAY DIFFRACTIONr_angle_other_deg2.3583785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.176550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.84925.29417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0411564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.384151
X-RAY DIFFRACTIONr_chiral_restr0.1380.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02446
X-RAY DIFFRACTIONr_gen_planes_other0.0140.0275
X-RAY DIFFRACTIONr_nbd_refined0.1740.1369
X-RAY DIFFRACTIONr_nbd_other0.1120.13313
X-RAY DIFFRACTIONr_nbtor_refined0.1450.1210
X-RAY DIFFRACTIONr_nbtor_other0.0620.1227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.050.135
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.1332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0550.119
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2382333
X-RAY DIFFRACTIONr_mcbond_other0.9122104
X-RAY DIFFRACTIONr_mcangle_it2.5023414
X-RAY DIFFRACTIONr_scbond_it2.6822181
X-RAY DIFFRACTIONr_scangle_it3.283132
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 68 -
Rwork0.17 716 -
obs--91.48 %
Refinement TLS params.Method: refined / Origin x: 9.138 Å / Origin y: -0.048 Å / Origin z: 3.471 Å
111213212223313233
T0.0212 Å20.005 Å20.0086 Å2--0.0296 Å2-0.0039 Å2---0.0375 Å2
L2.1979 °20.6432 °2-0.426 °2-1.3634 °2-0.4622 °2--1.968 °2
S-0.0388 Å °0.0098 Å °-0.0547 Å °0.001 Å °0.0506 Å °-0.0081 Å °0.0535 Å °-0.0577 Å °-0.0118 Å °

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