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- PDB-1r0r: 1.1 Angstrom Resolution Structure of the Complex Between the Prot... -

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Basic information

Entry
Database: PDB / ID: 1r0r
Title1.1 Angstrom Resolution Structure of the Complex Between the Protein Inhibitor, OMTKY3, and the Serine Protease, Subtilisin Carlsberg
Components
  • Ovomucoid
  • subtilisin carlsberg
KeywordsHYDROLASE / high resolution / serine protease / protein inhibitor
Function / homology
Function and homology information


subtilisin / molecular function inhibitor activity / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
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 / Subtilisin Carlsberg-like catalytic domain / 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 / Subtilisin Carlsberg-like catalytic domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin Carlsberg / Ovomucoid
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
Meleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsHorn, J.R. / Ramaswamy, S. / Murphy, K.P.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure and energetics of protein-protein interactions: the role of conformational heterogeneity in OMTKY3 binding to serine proteases
Authors: Horn, J.R. / Ramaswamy, S. / Murphy, K.P.
History
DepositionSep 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: subtilisin carlsberg
I: Ovomucoid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0526
Polymers32,8912
Non-polymers1604
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-44 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.329, 70.810, 127.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein subtilisin carlsberg


Mass: 27306.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin
#2: Protein Ovomucoid / / OMTKY3


Mass: 5585.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P68390
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium dihydrogen phosphate, 0.1 M Tris, and 50%(v/v) 2-methyl-2,4-pentanediol (MPD), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
220 mMMES1droppH6.0
3150 mM1dropKCl
40.2 Mammonium dihydrogen phosphate1reservoir
50.1 MTris1reservoirpH8.5
650 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.1→15.25 Å / Num. obs: 107101 / % possible obs: 94.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.01 % / Biso Wilson estimate: 8.1 Å2 / Rsym value: 0.094 / Net I/σ(I): 5.76
Reflection shellResolution: 1.1→1.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.01 / Num. unique all: 13901 / Rsym value: 0.24 / % possible all: 92.9
Reflection
*PLUS
Num. obs: 101307 / Num. measured all: 305107 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 92.9 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→15.25 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.635 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18404 1096 1 %RANDOM
Rwork0.15847 ---
obs0.15873 107101 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.227 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--1.2 Å20 Å2
3----0.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.033 Å0.032 Å
Luzzati d res low-15.25 Å
Luzzati sigma a0.033 Å0.032 Å
Refinement stepCycle: LAST / Resolution: 1.1→15.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 6 405 2773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212376
X-RAY DIFFRACTIONr_bond_other_d0.0010.022095
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9433244
X-RAY DIFFRACTIONr_angle_other_deg0.75134888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9663322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.82815368
X-RAY DIFFRACTIONr_chiral_restr0.0920.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022710
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02441
X-RAY DIFFRACTIONr_nbd_refined0.2430.3547
X-RAY DIFFRACTIONr_nbd_other0.190.32043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.5305
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2580.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.517
X-RAY DIFFRACTIONr_mcbond_it1.1291.51612
X-RAY DIFFRACTIONr_mcangle_it1.57322580
X-RAY DIFFRACTIONr_scbond_it2.3833764
X-RAY DIFFRACTIONr_scangle_it3.3594.5664
LS refinement shellResolution: 1.097→1.125 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.421 91
Rwork0.354 7438
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4680.0975-0.38180.2039-0.1650.75770.03820.05520.02330.02850.01510.0134-0.0621-0.0975-0.05330.06850.00560.00610.07030.00540.068625.7220.649.901
20.83670.6765-0.23362.99980.06550.5679-0.0071-0.0111-0.10360.0199-0.0447-0.19610.02670.00510.05180.0629-0.01730.01160.0617-0.00350.08626.301-2.9344.496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1EA1 - 2751 - 274
2X-RAY DIFFRACTION2IB6 - 561 - 51
Refinement
*PLUS
Rfactor Rfree: 0.184 / Rfactor Rwork: 0.1587
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.475

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