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- PDB-6fj2: Structure of Thermolysin solved from SAD data collected at the pe... -

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Basic information

Entry
Database: PDB / ID: 6fj2
TitleStructure of Thermolysin solved from SAD data collected at the peak of the Zn absorption edge on ID30B
ComponentsThermolysin
KeywordsHYDROLASE / Native
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 / Thermolysin metallopeptidase, alpha-helical 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
LYSINE / trimethylamine oxide / VALINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.43 Å
AuthorsMcCarthy, A.A. / Mueller-Dieckmann, C.
CitationJournal: J Synchrotron Radiat / Year: 2018
Title: ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF.
Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, ...Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, M. / Malbet-Monaco, S. / McSweeney, S. / Nurizzo, D. / Papp, G. / Rossi, C. / Sinoir, J. / Sorez, C. / Surr, J. / Svensson, O. / Zander, U. / Cipriani, F. / Theveneau, P. / Mueller-Dieckmann, C.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 8, 2018Group: Data collection / Database references / Category: citation_author / pdbx_related_exp_data_set
Item: _citation_author.identifier_ORCID / _pdbx_related_exp_data_set.data_reference
Revision 1.4Feb 20, 2019Group: Data collection / Derived calculations
Category: pdbx_data_processing_status / struct_conn / struct_conn_type

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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)35,22913
Polymers34,3601
Non-polymers86912
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.717, 92.717, 128.621
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-1408-

TMO

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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: Bacillus subtilis (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 7 types, 374 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9NO
#6: Chemical ChemComp-VAL / VALINE / Valine


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#7: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 46.68 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.05M MES, 1M NaCl, 45% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2017
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.43→80.3 Å / Num. obs: 60230 / % possible obs: 96.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.042 / Rrim(I) all: 0.096 / Net I/σ(I): 13.6
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2379 / CC1/2: 0.93 / Rpim(I) all: 0.137 / Rrim(I) all: 0.262 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.43→80.3 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.542 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.054
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16405 3000 5 %RANDOM
Rwork0.14425 ---
obs0.14523 57172 98.68 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 16.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.04 Å2-0 Å2
2---0.07 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.43→80.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 29 362 2840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022685
X-RAY DIFFRACTIONr_bond_other_d0.0020.022329
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9383652
X-RAY DIFFRACTIONr_angle_other_deg1.04435414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35924.504131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.115399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4751511
X-RAY DIFFRACTIONr_chiral_restr0.1090.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023092
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02575
X-RAY DIFFRACTIONr_mcbond_it1.0660.7691327
X-RAY DIFFRACTIONr_mcbond_other1.0390.7651320
X-RAY DIFFRACTIONr_mcangle_it1.3421.1471652
X-RAY DIFFRACTIONr_mcangle_other1.3421.1481653
X-RAY DIFFRACTIONr_scbond_it2.0360.9481355
X-RAY DIFFRACTIONr_scbond_other2.0350.951356
X-RAY DIFFRACTIONr_scangle_other2.3271.3651979
X-RAY DIFFRACTIONr_long_range_B_refined4.38110.5513172
X-RAY DIFFRACTIONr_long_range_B_other4.1759.7453090
LS refinement shellResolution: 1.428→1.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 172 -
Rwork0.19 3569 -
obs--85 %
Refinement TLS params.Method: refined / Origin x: 35.654 Å / Origin y: 50.104 Å / Origin z: -3.157 Å
111213212223313233
T0.0297 Å20.0108 Å2-0.0241 Å2-0.0331 Å2-0.003 Å2--0.0269 Å2
L1.1532 °20.2723 °2-0.3202 °2-0.402 °2-0.0696 °2--0.651 °2
S-0.0114 Å °0.0285 Å °0.0338 Å °0.0047 Å °-0.0144 Å °-0.0431 Å °-0.0505 Å °0.0546 Å °0.0258 Å °

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