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- PDB-3p7p: Radiation damage study of thermolysin - 100K structure A (0.1 MGy) -

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Basic information

Entry
Database: PDB / ID: 3p7p
TitleRadiation damage study of thermolysin - 100K structure A (0.1 MGy)
ComponentsThermolysin
KeywordsHYDROLASE / alpha/beta protein
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: 2.2 Å
AuthorsJuers, D.H. / Weik, M.
CitationJournal: To be Published
Title: Radiation damage study of thermolysin - 100K structure A (0.1 MGy)
Authors: Juers, D.H. / Weik, M.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 25, 2015Group: Other
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5886
Polymers34,3621
Non-polymers2265
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.220, 93.220, 128.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11E-525-

HOH

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Components

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34362.305 Da / Num. of mol.: 1 / Fragment: UNP residues 233-548 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 40% DMSO, pH 5.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.2→80.85 Å / Num. all: 17356 / Num. obs: 17356 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.325.80.0897.31440724770.089100
2.32-2.465.80.0897.11356523440.08999.9
2.46-2.635.80.0966.41272622100.096100
2.63-2.845.70.1025.91189520780.102100
2.84-3.115.60.1055.61075619270.105100
3.11-3.485.40.0936.1944917360.09399.9
3.48-4.025.10.0728789215500.07299.7
4.02-4.925.80.0678.7785313470.067100
4.92-6.965.70.0688.2600610540.06899.5
6.96-38.5195.10.0688.632096330.06898.2

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→80.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2323 / WRfactor Rwork: 0.1594 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8696 / SU B: 4.617 / SU ML: 0.119 / SU R Cruickshank DPI: 0.2392 / SU Rfree: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 876 5.1 %RANDOM
Rwork0.1488 ---
obs0.152 17341 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.14 Å2 / Biso mean: 11.5116 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→80.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 5 332 2769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212492
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9243394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61824.435124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06515357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.041510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021978
X-RAY DIFFRACTIONr_nbd_refined0.2070.21260
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2277
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.226
X-RAY DIFFRACTIONr_mcbond_it0.7731.51585
X-RAY DIFFRACTIONr_mcangle_it1.22522481
X-RAY DIFFRACTIONr_scbond_it2.24531062
X-RAY DIFFRACTIONr_scangle_it3.134.5913
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 73 -
Rwork0.134 1180 -
all-1253 -
obs--100 %

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