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- PDB-6ig7: Crystal structure of thermolysin delivered in polyacrylamide usin... -

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Basic information

Entry
Database: PDB / ID: 6ig7
TitleCrystal structure of thermolysin delivered in polyacrylamide using x-ray free electron laser
ComponentsThermolysin
KeywordsHYDROLASE / thermolysin / xfel / serial femtosecond crystallography / sfx / x-ray free electron laser
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
LEUCINE / LYSINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2019
Title: Polyacrylamide injection matrix for serial femtosecond crystallography.
Authors: Park, J. / Park, S. / Kim, J. / Park, G. / Cho, Y. / Nam, K.H.
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / diffrn_source ...atom_site / diffrn_source / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 2.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Aug 28, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_R_split
Revision 2.3Sep 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_R_split
Revision 2.4Sep 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 / _struct_conn.ptnr2_label_asym_id
Revision 2.5Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)34,8648
Polymers34,3601
Non-polymers5047
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-63 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.663, 92.663, 128.591
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 genetically manipulated source
Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria)
Gene: npr / Production host: Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 5 types, 149 molecules

#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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#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.: 142 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 277.5 K / Method: small tubes / Details: Tris-HCl, NaCl

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.2792 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 19, 2018 / Frequency: 30 / Details: KB mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2792 Å / Relative weight: 1
ReflectionResolution: 1.8→131.57 Å / Num. obs: 30878 / % possible obs: 100 % / Redundancy: 663.8 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 0.99 / R split: 0.1463 / Net I/σ(I): 4.67
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 471 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 3028 / CC1/2: 0.61 / R split: 0.8409 / % possible all: 100
Serial crystallography measurementCollection time total: 2.11 hours / Collimation: Kirkpatrick-Baez mirrors / Focal spot size: 5 µm2 / Pulse duration: 20 fsec. / Pulse photon energy: 9.7 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: injector / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: polyacrylamide / Crystal conc.: 36000000 / Description: CMD (carrier matrix delivery) injector / Flow rate: 800 µL/min / Injector diameter: 100 µm / Injector nozzle: gas / Injector temperature: 296 K / Jet diameter: 100 µm / Power by: HPLC
Preparation: crystals delivered in polyacrylamide injection matrix at room temperature
Serial crystallography data reductionCrystal hits: 47865 / Frame hits: 47865 / Frames failed index: 25652 / Frames indexed: 22213 / Frames total: 228304 / Lattices indexed: 22213

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHASERphasing
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DM9

5dm9


Resolution: 1.8→40.124 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 855 2.77 %
Rwork0.1727 --
obs0.1735 30866 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 5 142 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112515
X-RAY DIFFRACTIONf_angle_d1.0043425
X-RAY DIFFRACTIONf_dihedral_angle_d11.9131435
X-RAY DIFFRACTIONf_chiral_restr0.056365
X-RAY DIFFRACTIONf_plane_restr0.006452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.39541390.30974902X-RAY DIFFRACTION100
1.9128-2.06050.28221400.21364903X-RAY DIFFRACTION100
2.0605-2.26780.20011410.17324929X-RAY DIFFRACTION100
2.2678-2.59590.21841410.17454971X-RAY DIFFRACTION100
2.5959-3.27040.18871430.17345017X-RAY DIFFRACTION100
3.2704-40.13420.18061510.1565289X-RAY DIFFRACTION100

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