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- PDB-3vyv: Crystal structure of subtilisin NAT at 1.36 -

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Basic information

Entry
Database: PDB / ID: 3vyv
TitleCrystal structure of subtilisin NAT at 1.36
ComponentsSubtilisin NAT
KeywordsHYDROLASE / Bacillus subtilis subsp. natto / serine protease / O-Benzylsulfonyl-serine
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / 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. ...Subtilisin Carlsberg-like catalytic domain / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. natto (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsUshijima, H. / Fuchita, N. / Kajiwara, T. / Motoshima, H. / Ueno, G. / Watanabe, K.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of subtilisin NAT at 1.36
Authors: Watanabe, K.
History
DepositionOct 3, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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 NAT
B: Subtilisin NAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1428
Polymers55,7982
Non-polymers3456
Water7,350408
1
A: Subtilisin NAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1635
Polymers27,8991
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Subtilisin NAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9793
Polymers27,8991
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.682, 80.039, 87.449
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 NAT / Nattokinase


Mass: 27898.797 Da / Num. of mol.: 2 / Fragment: UNP residues 107-381 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis subsp. natto (bacteria) / Strain: subsp. natto / References: UniProt: P35835, subtilisin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG6000, 5% Ethanol, 0.2M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 23, 2010
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. obs: 111769 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 37.9
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.6 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
d*TREKdata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1scj

1scj


Resolution: 1.36→46.07 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.189 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17616 5589 5 %RANDOM
Rwork0.14645 ---
obs0.1479 106057 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.993 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.36→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 16 408 4350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214016
X-RAY DIFFRACTIONr_bond_other_d0.0070.022510
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.955488
X-RAY DIFFRACTIONr_angle_other_deg3.336192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.99225.294136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79615560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.212158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214610
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02744
X-RAY DIFFRACTIONr_mcbond_it1.9091.52710
X-RAY DIFFRACTIONr_mcbond_other0.8551.51146
X-RAY DIFFRACTIONr_mcangle_it2.66424332
X-RAY DIFFRACTIONr_scbond_it4.31331306
X-RAY DIFFRACTIONr_scangle_it5.7754.51156
X-RAY DIFFRACTIONr_rigid_bond_restr2.0636526
LS refinement shellResolution: 1.36→1.393 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 389 -
Rwork0.171 7443 -
obs--95.54 %

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