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- PDB-4m65: In situ thermolysin crystallized on a MiTeGen micromesh with aspa... -

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Basic information

Entry
Database: PDB / ID: 4m65
TitleIn situ thermolysin crystallized on a MiTeGen micromesh with asparagine ligand
ComponentsThermolysin
KeywordsHYDROLASE / ASPARAGINE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / Peptidase M4, C-terminal / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily ...Elastase; domain 1 - #10 / Elastase; domain 1 / Peptidase M4, C-terminal / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ASPARAGINE / HYDROSULFURIC ACID / Neutral metalloproteinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Agarwal, R. / Allaire, M. ...Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Agarwal, R. / Allaire, M. / Orville, A.M. / Jackimowicz, R. / Ma, M.Y. / Sweet, R.M. / Soares, A.S.
CitationJournal: Acta Crystallogr.,Sect.D
Title: Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes
Authors: Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Agarwal, R. / Allaire, M. / Orville, A.M. / Jackimowicz, R. / Ma, M.Y. / ...Authors: Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Agarwal, R. / Allaire, M. / Orville, A.M. / Jackimowicz, R. / Ma, M.Y. / Sweet, R.M. / Soares, A.S.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Sep 20, 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_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_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)35,58221
Polymers34,4331
Non-polymers1,14920
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.831, 92.831, 129.171
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-566-

HOH

21A-612-

HOH

31A-629-

HOH

41A-673-

HOH

51A-700-

HOH

61A-769-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thermolysin /


Mass: 34433.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: V5IRV7*PLUS

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Non-polymers , 6 types, 480 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / 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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ASN / ASPARAGINE / Asparagine


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 290 K / Method: in situ crystallization on micromesh / pH: 7.5
Details: 1.45M calcium chloride, 45% DMSO, 50mM TRIS pH 7.5, In situ crystallization on micromesh, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C11.1
SYNCHROTRONNSLS X2521.1
SYNCHROTRONNSLS X29A31.075
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDAug 4, 2013
DECTRIS PILATUS 6M2PIXEL
ADSC QUANTUM 3153CCD
RadiationMonochromator: 1.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.0751
ReflectionResolution: 1.6→31.59 Å / Num. all: 43577 / Num. obs: 43035 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 28.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 58.4

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4TLN

4tln


Resolution: 1.6→31.59 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.081 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15928 2167 5 %RANDOM
Rwork0.13008 ---
all0.1316 43035 --
obs0.1316 40851 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.678 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.43 Å2-0 Å2
2---0.43 Å2-0 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 61 460 2952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192598
X-RAY DIFFRACTIONr_bond_other_d0.0020.022315
X-RAY DIFFRACTIONr_angle_refined_deg2.5591.9313528
X-RAY DIFFRACTIONr_angle_other_deg1.12835312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07224.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66615372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9711511
X-RAY DIFFRACTIONr_chiral_restr0.1640.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5181.3031296
X-RAY DIFFRACTIONr_mcbond_other1.5171.3031295
X-RAY DIFFRACTIONr_mcangle_it2.0041.9581626
X-RAY DIFFRACTIONr_mcangle_other2.0041.9581627
X-RAY DIFFRACTIONr_scbond_it2.9831.5691302
X-RAY DIFFRACTIONr_scbond_other2.9831.5691302
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1572.2291898
X-RAY DIFFRACTIONr_long_range_B_refined7.36313.7513490
X-RAY DIFFRACTIONr_long_range_B_other6.55512.2253260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.602→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 162 -
Rwork0.17 2895 -
obs--96.44 %

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