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- PDB-4cg0: Savinase crystal structures for combined single crystal diffracti... -

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Basic information

Entry
Database: PDB / ID: 4cg0
TitleSavinase crystal structures for combined single crystal diffraction and powder diffraction analysis
ComponentsSUBTILISIN SAVINASE
KeywordsHYDROLASE / SINGLE CRYSTAL ANALYSIS / POWDER DIFFRACTION / QUALITY CONTROL / MICROCRYSTALLINE SUSPENSION
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / : / 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 / Peptidase S8, subtilisin-related ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / : / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS LENTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsFrankaer, C.G. / Moroz, O.V. / Turkenburg, J.P. / Aspmo, S.I. / Thymark, M. / Friis, E.P. / Stahla, K. / Nielsen, J.E. / Wilson, K.S. / Harris, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Analysis of an Industrial Production Suspension of Bacillus Lentus Subtilisin Crystals by Powder Diffraction: A Powerful Quality-Control Tool.
Authors: Frankaer, C.G. / Moroz, O.V. / Turkenburg, J.P. / Aspmo, S.I. / Thymark, M. / Friis, E.P. / Stahl, K. / Nielsen, J.E. / Wilson, K.S. / Harris, P.
History
DepositionNov 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_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 SAVINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7813
Polymers26,7181
Non-polymers632
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.040, 57.550, 71.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SUBTILISIN SAVINASE / ALKALINE PROTEASE


Mass: 26718.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS LENTUS (bacteria) / Production host: BACILLUS LICHENIFORMIS (bacteria) / References: UniProt: P29600, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.7 % / Description: NONE
Crystal growDetails: CRYSTALS FROM INDUSTRIAL PRODUCTION SUSPENSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.36→17.8 Å / Num. obs: 46289 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.9
Reflection shellResolution: 1.36→1.4 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / % possible all: 78.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SVN

1svn


Resolution: 1.36→44.8 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.055 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15413 2345 5.1 %RANDOM
Rwork0.10908 ---
obs0.11133 43917 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.461 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.36→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 2 369 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192010
X-RAY DIFFRACTIONr_bond_other_d0.0010.021849
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9332765
X-RAY DIFFRACTIONr_angle_other_deg1.16234249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34824.93273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57415276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.385159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212497
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02466
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7991.191135
X-RAY DIFFRACTIONr_mcbond_other1.7971.1891134
X-RAY DIFFRACTIONr_mcangle_it2.1211.7991438
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5191.458875
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.25633859
X-RAY DIFFRACTIONr_sphericity_free42.2995100
X-RAY DIFFRACTIONr_sphericity_bonded10.25754084
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 132 -
Rwork0.199 2549 -
obs--77.06 %

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