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- PDB-3unx: Bond length analysis of asp, glu and his residues in subtilisin C... -

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Basic information

Entry
Database: PDB / ID: 3unx
TitleBond length analysis of asp, glu and his residues in subtilisin Carlsberg at 1.26A resolution
ComponentsSubtilisin Carlsberg
KeywordsHYDROLASE
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / extracellular region / 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
Subtilisin Carlsberg
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsFisher, S.J. / Helliwell, J.R. / Blakeley, M.P. / Cianci, M. / McSweeny, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness.
Authors: Fisher, S.J. / Blakeley, M.P. / Cianci, M. / McSweeney, S. / Helliwell, J.R.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7518
Polymers27,2791
Non-polymers4727
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.099, 55.159, 75.453
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 Carlsberg


Mass: 27279.176 Da / Num. of mol.: 1 / Fragment: mature form (UNP residues 106-379)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: apr / Production host: Escherichia coli (E. coli) / References: UniProt: P00780, subtilisin
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 265 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 298 K / Method: batch / pH: 7.5
Details: 13% w/v sodium sulfate, pH 7.5, BATCH, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.26→13.79 Å / Num. obs: 59740 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.5
Reflection shellResolution: 1.26→1.33 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.2 / Num. unique all: 7587 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
MLPHAREphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3L

1c3l


Resolution: 1.26→13.79 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 10.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1392 3011 5.08 %RANDOM
Rwork0.1181 ---
obs0.1192 59740 100 %-
all-59740 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.096 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3629 Å20 Å20 Å2
2--0.0614 Å2-0 Å2
3---0.3014 Å2
Refinement stepCycle: LAST / Resolution: 1.26→13.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 27 265 2210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112128
X-RAY DIFFRACTIONf_angle_d1.4952936
X-RAY DIFFRACTIONf_dihedral_angle_d11.616769
X-RAY DIFFRACTIONf_chiral_restr0.195348
X-RAY DIFFRACTIONf_plane_restr0.008384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.27970.25481200.21152531X-RAY DIFFRACTION100
1.2797-1.30070.24021150.19092539X-RAY DIFFRACTION100
1.3007-1.32310.18591460.17122517X-RAY DIFFRACTION100
1.3231-1.34710.21341350.15152538X-RAY DIFFRACTION100
1.3471-1.3730.18211430.1452539X-RAY DIFFRACTION100
1.373-1.4010.16971360.13452512X-RAY DIFFRACTION100
1.401-1.43140.16071320.11712540X-RAY DIFFRACTION100
1.4314-1.46470.16261440.10092519X-RAY DIFFRACTION100
1.4647-1.50130.15521200.09132563X-RAY DIFFRACTION100
1.5013-1.54180.12951410.08472531X-RAY DIFFRACTION100
1.5418-1.58710.11031550.08622524X-RAY DIFFRACTION100
1.5871-1.63830.11781230.08262560X-RAY DIFFRACTION100
1.6383-1.69670.12271330.08572545X-RAY DIFFRACTION100
1.6967-1.76450.12021470.08122564X-RAY DIFFRACTION100
1.7645-1.84470.11671350.09162555X-RAY DIFFRACTION100
1.8447-1.94170.12281510.09182555X-RAY DIFFRACTION100
1.9417-2.0630.10071280.09212561X-RAY DIFFRACTION100
2.063-2.22160.11911470.09332584X-RAY DIFFRACTION100
2.2216-2.44410.1071470.09752570X-RAY DIFFRACTION100
2.4441-2.79520.13261390.10782606X-RAY DIFFRACTION100
2.7952-3.5120.13741320.11872641X-RAY DIFFRACTION100
3.512-13.79060.16431420.18312661X-RAY DIFFRACTION97

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