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- PDB-5wr5: Thermolysin, liganded form with cryo condition 1 -

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Basic information

Entry
Database: PDB / ID: 5wr5
TitleThermolysin, liganded form with cryo condition 1
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1Nov 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
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

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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)35,2429
Polymers34,3601
Non-polymers8818
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-26 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.246, 92.246, 129.718
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-768-

HOH

21A-840-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 392 molecules

#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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG2000MME, MES, CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.1 Å / Num. obs: 26366 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.56 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OW3

4ow3


Resolution: 1.9→43.5 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / Phase error: 16.99
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1246 4.73 %Random selection
Rwork0.154 ---
obs0.155 26363 100 %-
Displacement parametersBiso mean: 22.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 50 384 2866
LS refinement shellResolution: 1.9→1.98 Å
RfactorNum. reflection% reflection
Rfree0.257 131 -
Rwork0.201 2735 -
obs--100 %

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