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- PDB-1yu6: Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex -

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Basic information

Entry
Database: PDB / ID: 1yu6
TitleCrystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex
Components
  • Ovomucoid
  • Subtilisin Carlsberg
KeywordsHYDROLASE / protein proteinase inhibitor / protease
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-type serine protease inhibitor domain / 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. ...Proteinase inhibitor I1, Kazal-type, metazoa / Kazal-type serine protease inhibitor domain / 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 speciesMeleagris gallopavo (turkey)
Bacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMaynes, J.T. / Cherney, M.M. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.
Authors: Maynes, J.T. / Cherney, M.M. / Qasim, M.A. / Laskowski Jr, M. / James, M.N.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin Carlsberg
B: Subtilisin Carlsberg
C: Ovomucoid
D: Ovomucoid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3106
Polymers95,2304
Non-polymers802
Water5,927329
1
A: Subtilisin Carlsberg
C: Ovomucoid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6553
Polymers47,6152
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-9 kcal/mol
Surface area11960 Å2
MethodPISA
2
B: Subtilisin Carlsberg
D: Ovomucoid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6553
Polymers47,6152
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-10 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.256, 100.971, 115.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTwo biological units are in the asymmetric unit

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Components

#1: Protein Subtilisin Carlsberg


Mass: 27437.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin
#2: Protein Ovomucoid /


Mass: 20177.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 10% ethylene glycol, 480 mM sodium malate, 75 mM sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2003 / Details: Mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→74.54 Å / Num. all: 88530 / Num. obs: 88530 / % possible obs: 95.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.102 / Rsym value: 0.266 / Net I/σ(I): 14.7
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.21 / Num. unique all: 7071 / % possible all: 77.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VSB and 1CHO

1vsb

1cho


Resolution: 1.55→74.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.382 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.08 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20518 4428 5 %RANDOM
Rwork0.19129 ---
all0.19199 88530 --
obs0.19199 84093 85.69 %-
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: 12.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.78 Å20 Å2
3---0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.08 Å0.085 Å
Refinement stepCycle: LAST / Resolution: 1.55→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4607 0 2 329 4938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214693
X-RAY DIFFRACTIONr_bond_other_d0.0110.024099
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9456396
X-RAY DIFFRACTIONr_angle_other_deg1.15239558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875645
X-RAY DIFFRACTIONr_chiral_restr0.1010.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025437
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02883
X-RAY DIFFRACTIONr_nbd_refined0.1870.3977
X-RAY DIFFRACTIONr_nbd_other0.2020.34868
X-RAY DIFFRACTIONr_nbtor_other0.0830.52754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.5428
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.59
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.355
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.533
X-RAY DIFFRACTIONr_mcbond_it0.5511.53191
X-RAY DIFFRACTIONr_mcangle_it1.06125069
X-RAY DIFFRACTIONr_scbond_it1.92931502
X-RAY DIFFRACTIONr_scangle_it3.1894.51327
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 116 -
Rwork0.211 2057 -
obs-2173 77.3 %

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