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- PDB-9p17: Thermolysin Room-Temperature In-Situ, Shipped -

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Basic information

Entry
Database: PDB / ID: 9p17
TitleThermolysin Room-Temperature In-Situ, Shipped
ComponentsThermolysin
KeywordsHYDROLASE / thermostable / metalloprotease
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
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 ...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 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
PHOSPHATE ION / Thermolysin
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCampomizzi, C.S. / Snell, M.E. / Mikolajek, H. / Sandy, J. / Sanchez-Weatherby, J. / Budziszewski, G.R. / Hough, M.A. / Bowman, S.E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141273 United States
CitationJournal: Biorxiv / Year: 2025
Title: Does crossing the pond affect crystal quality?
Authors: Campomizzi, C.S. / Snell, M.E. / Mikolajek, H. / Sandy, J. / Sanchez-Weatherby, J. / Budziszewski, G.R. / Russi, S. / Howells Jr., R. / Cohen, A. / Hough, M.A. / Bowman, S.E.J.
History
DepositionJun 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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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)34,7218
Polymers34,3601
Non-polymers3617
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.032, 93.032, 130.452
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Thermolysin / Neutral protease


Mass: 34360.336 Da / Num. of mol.: 1
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-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.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.20 M sodium di-hydrogen phosphate, 16.7% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Sep 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.66→80.57 Å / Num. obs: 39612 / % possible obs: 98.8 % / Redundancy: 10.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Χ2: 0.58 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.09-80.579.70.03861.33250.9990.0150.0411.54100
1.66-1.694.61.6110.517680.3681.0241.9340.2991

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
Aimlessdata scaling
Cootmodel building
xia2.multiplexdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→80.568 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.083 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1831 1991 5.035 %
Rwork0.1605 37554 -
all0.162 --
obs-39545 98.865 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.164 Å2-0.082 Å2-0 Å2
2---0.164 Å20 Å2
3---0.534 Å2
Refinement stepCycle: LAST / Resolution: 1.66→80.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 11 228 2659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122499
X-RAY DIFFRACTIONr_angle_refined_deg1.781.7733408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1715319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.508510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06110353
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0510122
X-RAY DIFFRACTIONr_chiral_restr0.0950.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021990
X-RAY DIFFRACTIONr_nbd_refined0.2270.21195
X-RAY DIFFRACTIONr_nbtor_refined0.3230.21801
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2238
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3310.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2720.247
X-RAY DIFFRACTIONr_mcbond_it1.711.7661273
X-RAY DIFFRACTIONr_mcangle_it2.3243.1581593
X-RAY DIFFRACTIONr_scbond_it3.2182.1141226
X-RAY DIFFRACTIONr_scangle_it5.033.6951815
X-RAY DIFFRACTIONr_lrange_it10.97724.3454147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.66-1.7030.3631020.34325470.34428820.8750.89891.91530.341
1.703-1.750.3661240.31625710.31828270.8750.91695.33070.313
1.75-1.8010.2781240.27225890.27227660.9440.94598.08390.262
1.801-1.8560.2681330.23925070.24126700.9530.95998.87640.224
1.856-1.9170.2271340.20424560.20525950.9660.97199.80730.182
1.917-1.9840.1741220.17823960.17825190.9770.97899.96030.156
1.984-2.0590.2071260.17522950.17624210.9710.981000.153
2.059-2.1430.1781170.16122400.16223570.9770.9841000.137
2.143-2.2380.1931200.15121310.15322510.9780.9851000.129
2.238-2.3470.2051300.14620340.1521640.9740.9871000.123
2.347-2.4740.1931220.15219440.15520660.9790.9861000.125
2.474-2.6240.2041000.15618550.15819550.9740.9851000.133
2.624-2.8050.164960.1517560.1518520.9850.9861000.125
2.805-3.0290.215830.1516470.15317300.9730.9861000.129
3.029-3.3180.138850.15515130.15415980.9870.9851000.133
3.318-3.7090.162810.12713850.12914660.9840.9911000.114
3.709-4.2810.131710.11212310.11313020.9910.9941000.102
4.281-5.240.125540.10610710.10711250.9910.9941000.095
5.24-7.3950.145430.1528520.1518950.9790.9891000.136
7.395-80.5680.172240.1485330.1495570.990.9891000.151

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