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- PDB-1gxw: the 2.2 A resolution structure of thermolysin crystallized in pre... -

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Basic information

Entry
Database: PDB / ID: 1gxw
Titlethe 2.2 A resolution structure of thermolysin crystallized in presence of potassium thiocyanate
ComponentsTHERMOLYSIN
KeywordsHYDROLASE / THERMOLYSIN / METALLOENDOPEPTIDASE / THIOCYANATE / SALTING-IN / METALLOPROTEASE
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 / Thermolysin metallopeptidase, alpha-helical 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 / THIOCYANATE ION / VALINE / Thermolysin
Similarity search - Component
Biological speciesBACILLUS THERMOPROTEOLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGaucher, J.F. / Selkti, M. / Prange, T. / Tomas, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The 2.2 A Resolution Structure of Thermolysin (Tln) Crystallized in the Presence of Potassium Thiocyanate.
Authors: Gaucher, J. / Selkti, M. / Prange, T. / Tomas, A.
#1: Journal: J.Biochem. / Year: 1998
Title: Effect of Salts on the Solubility of Thermolysin: A Remarkable Increase in the Solubility as Well as the Activity by the Addition of Salts without Aggregation or Dispersion of Thermolysin
Authors: Inouye, K. / Kuzuya, K. / Tonomura, B.
#2: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Thermolysin Refined at 1.6A Resolution
Authors: Holmes, M.A. / Matthews, B.W.
History
DepositionApr 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2002Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)34,9109
Polymers34,3621
Non-polymers5488
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.170, 93.170, 130.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsTHE BIOMOLECULE CONSISTS OF A DI-PEPTIDE BURIED WITHINTHE PROTEIN. THE BOUND SURFACE AREA BETWEEN THE TWOCHAINS IS 947.8 ANGSTROM**2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THERMOLYSIN /


Mass: 34362.305 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 , 6 types, 178 molecules

#2: Chemical ChemComp-VAL / VALINE / Valine


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


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.38 Å3/Da / Density % sol: 38.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.3
Details: 0.5MICROL HANGING DROP CONTAINING 87MG/ML OF THERMOLYSIN IN BUFFER A (50MM TRIS/HCL PH8.3, 1M KSCN, 20MM CACL2) WAS EQUILIBRATED AGAINST 740MICROL BUFFER A AND 260MICROL WATER (SALTING-IN METHOD), pH 8.30
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
187 mg/mlprotein1drop
250 mMTHAM1reservoirpH8.3
31 MKSCN1reservoir
420 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 1.375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 2.18→19 Å / Num. obs: 15898 / % possible obs: 92.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.3
Reflection shellResolution: 2.18→2.32 Å / % possible all: 83.9
Reflection
*PLUS
Lowest resolution: 18.5 Å / % possible obs: 92.2 % / Num. measured all: 58898
Reflection shell
*PLUS
Lowest resolution: 2.3 Å / % possible obs: 82.7 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8TLN

8tln


Resolution: 2.18→18.46 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2790416.67 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1703 10.2 %RANDOM
Rwork0.163 ---
obs0.163 16715 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 105.015 Å2 / ksol: 0.590377 e/Å3
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-3.17 Å20 Å2
2---0.72 Å20 Å2
3---1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.18→18.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 25 170 2627
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.572
X-RAY DIFFRACTIONc_scangle_it3.522.5
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 261 10.6 %
Rwork0.183 2198 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4SCN.PARAM
Refinement
*PLUS
Lowest resolution: 19 Å / Rfactor Rfree: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rfree: 0.242

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