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- PDB-5wr3: Thermolysin, SFX liganded form with water-based carrier -

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Basic information

Entry
Database: PDB / ID: 5wr3
TitleThermolysin, SFX liganded form with water-based carrier
ComponentsThermolysin
KeywordsHYDROLASE / X-ray free-electron laser / Serial femtosecond crystallography / Microcrystal / Structure-based drug design
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
N-[(benzyloxy)carbonyl]-L-aspartic acid / Thermolysin
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKunishima, N. / Naitow, H. / Matsuura, Y.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation
Authors: Naitow, H. / Matsuura, Y. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Kobayashi, J. / Nango, E. / Iwata, S. / Kunishima, N.
History
DepositionNov 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / 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.ptnr2_auth_seq_id
Revision 1.3Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8537
Polymers34,3601
Non-polymers4936
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-25 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.590, 93.590, 131.220
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-727-

HOH

21A-745-

HOH

31A-781-

HOH

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Components

#1: Protein Thermolysin / Neutral protease


Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP residues 236-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: nprS, nprM / Production host: Geobacillus stearothermophilus (bacteria) / References: UniProt: P43133, thermolysin
#2: Chemical ChemComp-NX6 / N-[(benzyloxy)carbonyl]-L-aspartic acid


Mass: 267.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO6
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.5 / Details: PEG2000MME, MES, CaCl2

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.1→46.8 Å / Num. obs: 20466 / % possible obs: 100 % / Redundancy: 596.2 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 0.981 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 171.2 % / Mean I/σ(I) obs: 3.7 / CC1/2: 0.868 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OW3

4ow3


Resolution: 2.1→44.1 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / Phase error: 14.63
RfactorNum. reflection% reflectionSelection details
Rfree0.16 1006 4.92 %Random selection
Rwork0.126 ---
obs0.128 20453 99.4 %-
Displacement parametersBiso mean: 30.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 24 282 2738
LS refinement shellResolution: 2.1→2.21 Å
RfactorNum. reflection% reflection
Rfree0.206 140 -
Rwork0.159 2703 -
obs--100 %

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