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- PDB-3do2: Thermolysin by LB nanotemplate method after high X-Ray dose on ES... -

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Basic information

Entry
Database: PDB / ID: 3do2
TitleThermolysin by LB nanotemplate method after high X-Ray dose on ESRF ID14-2 beamline
ComponentsThermolysin
KeywordsHYDROLASE / metalloproteinase / Calcium / Metal-binding / Metalloprotease / Protease / Secreted / Zinc / Zymogen
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
LYSINE / VALINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 Å
AuthorsPechkova, E. / Tripathi, S.K. / Nicolini, C.
CitationJournal: To be Published
Title: Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective
Authors: Pechkova, E. / Tripathi, S.K. / Nicolini, C.
History
DepositionJul 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Derived calculations / Category: reflns_shell / struct_conn
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 1, 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 / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8508
Polymers34,3601
Non-polymers4907
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.562, 92.562, 128.712
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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 natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 5 types, 192 molecules

#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: Chemical ChemComp-VAL / VALINE


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


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


Mass: 18.015 Da / Num. of mol.: 185 / 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: 46.9 % / Mosaicity: 0.52 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: DMSO, Ammonium sulfate, MES, hanging drop, 293K, pH6.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2007 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.194→80.161 Å / Num. obs: 89247 / % possible obs: 84 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.238 / Rsym value: 0.238 / Net I/σ(I): 2.9
Reflection shellResolution: 1.18→1.25 Å / Redundancy: 1.3 % / Num. measured all: 6087 / Num. unique all: 4653 / % possible all: 30.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DNZ

3dnz


Resolution: 1.22→68.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.802 / SU B: 1.289 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2911 5.1 %RANDOM
Rwork0.238 ---
obs0.239 57583 59.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.95 Å2 / Biso mean: 16.835 Å2 / Biso min: 10.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.38 Å20 Å2
2---0.75 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.22→68.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 22 185 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212561
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9243496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0875328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36824.444126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84315369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4391510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022046
X-RAY DIFFRACTIONr_nbd_refined0.2230.31313
X-RAY DIFFRACTIONr_nbtor_refined0.320.51806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.5359
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.516
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.527
X-RAY DIFFRACTIONr_mcbond_it0.81721623
X-RAY DIFFRACTIONr_mcangle_it1.29532563
X-RAY DIFFRACTIONr_scbond_it1.01321082
X-RAY DIFFRACTIONr_scangle_it1.53933
LS refinement shellResolution: 1.219→1.251 Å / Total num. of bins used: 20 /
RfactorNum. reflection% reflection
Rwork0.713 6 -
obs--9 %

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