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- PDB-5o8n: Structure of thermolysin at room temperature via a method of acou... -

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Basic information

Entry
Database: PDB / ID: 5o8n
TitleStructure of thermolysin at room temperature via a method of acoustically induced rotation.
ComponentsThermolysin
KeywordsHYDROLASE / Zinc protease
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAxford, D.N. / Burton, C. / Docker, P. / Prince, M. / Topham, P.D.
CitationJournal: Lab Chip / Year: 2017
Title: An acoustic on-chip goniometer for room temperature macromolecular crystallography.
Authors: Burton, C.G. / Axford, D. / Edwards, A.M.J. / Gildea, R.J. / Morris, R.H. / Newton, M.I. / Orville, A.M. / Prince, M. / Topham, P.D. / Docker, P.T.
History
DepositionJun 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,80714
Polymers34,3601
Non-polymers44713
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-143 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.552, 93.552, 129.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-410-

NA

21A-411-

NA

31A-593-

HOH

41A-603-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria)
Gene: npr / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 5 types, 121 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Well solution: 1.2M Ammonium sulphate. Protein solution: 50mg/ml thermolysin, 50mM MES, 45% DMSO, 0.5M NaCl.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2017 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→44.02 Å / Num. obs: 26888 / % possible obs: 99.2 % / Redundancy: 61.2 % / Rmerge(I) obs: 0.427 / Net I/σ(I): 2.19
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 42.1 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 0.19 / Num. unique obs: 1316 / CC1/2: 0.29 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DIALSdata reduction
cctbx.primedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UU9

5uu9


Resolution: 1.9→44.004 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.78
RfactorNum. reflection% reflection
Rfree0.2586 1798 7.37 %
Rwork0.1995 --
obs0.2038 24405 90.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 13 108 2552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072545
X-RAY DIFFRACTIONf_angle_d0.8673471
X-RAY DIFFRACTIONf_dihedral_angle_d2.811944
X-RAY DIFFRACTIONf_chiral_restr0.05369
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.4214500.3962654X-RAY DIFFRACTION34
1.9514-2.00880.3729840.3631047X-RAY DIFFRACTION56
2.0088-2.07360.39581330.35431725X-RAY DIFFRACTION91
2.0736-2.14780.37551450.33731826X-RAY DIFFRACTION97
2.1478-2.23370.36961510.31941895X-RAY DIFFRACTION100
2.2337-2.33540.35951510.28611893X-RAY DIFFRACTION100
2.3354-2.45850.33661520.25341906X-RAY DIFFRACTION100
2.4585-2.61250.3171500.24821901X-RAY DIFFRACTION100
2.6125-2.81420.29561540.22041911X-RAY DIFFRACTION99
2.8142-3.09740.29321520.20561908X-RAY DIFFRACTION99
3.0974-3.54540.25831550.17551931X-RAY DIFFRACTION99
3.5454-4.46610.20181560.13921948X-RAY DIFFRACTION98
4.4661-44.01590.20641650.16772062X-RAY DIFFRACTION97

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