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- PDB-5uu7: Tetragonal thermolysin (295 K) in the presence of 50% mpd -

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Basic information

Entry
Database: PDB / ID: 5uu7
TitleTetragonal thermolysin (295 K) in the presence of 50% mpd
ComponentsThermolysin
KeywordsHYDROLASE / zinc protease / alpha/beta
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 / MOLECULAR REPLACEMENT / Resolution: 1.60001390701 Å
AuthorsJuers, D.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.
Authors: Juers, D.H. / Farley, C.A. / Saxby, C.P. / Cotter, R.A. / Cahn, J.K.B. / Holton-Burke, R.C. / Harrison, K. / Wu, Z.
History
DepositionFeb 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Mar 6, 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
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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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

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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)35,51319
Polymers34,3601
Non-polymers1,15318
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-322 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.026, 98.026, 107.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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 , 7 types, 271 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.76 Å3/Da / Density % sol: 67.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Protein: 50 mg/mL in 45% DMSO, 0.5 M ZnCl2 Well: ~2 M AmSO4

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Nov 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→20.8 Å / Num. obs: 131139 / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.4059349642 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellHighest resolution: 1.6 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.536 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CrysalisProdata collection
CrysalisProdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.60001390701→20.758774984 Å / SU ML: 0.161938408893 / Cross valid method: FREE R-VALUE / σ(F): 1.33421409687 / Phase error: 17.0203484588
RfactorNum. reflection% reflection
Rfree0.156491093947 3983 3.04059727926 %
Rwork0.144493900079 --
obs0.144862439573 130994 99.213826951 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.8901447676 Å2
Refinement stepCycle: LAST / Resolution: 1.60001390701→20.758774984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 42 253 2727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00787480230552620
X-RAY DIFFRACTIONf_angle_d0.9140285632253595
X-RAY DIFFRACTIONf_chiral_restr0.0565553827655388
X-RAY DIFFRACTIONf_plane_restr0.0061229781725469
X-RAY DIFFRACTIONf_dihedral_angle_d9.86574602161516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61950.3454627192341410.3355303765244373X-RAY DIFFRACTION95.737009544
1.6195-1.640.3078520733911420.3157007646994465X-RAY DIFFRACTION97.813163482
1.64-1.66160.3730749503391440.3126295183314526X-RAY DIFFRACTION98.6897717667
1.6616-1.68430.2687563205411380.2968584035654496X-RAY DIFFRACTION98.6587183308
1.6843-1.70840.3121340897261400.2866671885624522X-RAY DIFFRACTION98.7711864407
1.7084-1.73390.2731320219231450.2756616379634554X-RAY DIFFRACTION99.0514333895
1.7339-1.7610.2181474984011450.2599816174514510X-RAY DIFFRACTION99.3172605078
1.761-1.78980.2382418252891390.2445683937064561X-RAY DIFFRACTION99.4077834179
1.7898-1.82070.228132872291410.2324321150434574X-RAY DIFFRACTION99.493564043
1.8207-1.85370.2413943883911440.2089583484124500X-RAY DIFFRACTION99.4219653179
1.8537-1.88940.1940395891211410.1985118704924590X-RAY DIFFRACTION99.6839443742
1.8894-1.92790.1590498887491470.1806611049974528X-RAY DIFFRACTION99.765258216
1.9279-1.96980.2136359492261440.1694737552754588X-RAY DIFFRACTION99.7891185154
1.9698-2.01560.1968230029461400.1621713918544545X-RAY DIFFRACTION99.872095502
2.0156-2.06590.1834835321181440.1606514162734570X-RAY DIFFRACTION99.9364002544
2.0659-2.12170.1467595863211410.1427286246344547X-RAY DIFFRACTION99.9573560768
2.1217-2.18410.1356303334661440.1331234198444561X-RAY DIFFRACTION99.7879109226
2.1841-2.25450.1446761235441460.1281591204244551X-RAY DIFFRACTION99.7875504568
2.2545-2.3350.1316390018771330.1212752289334616X-RAY DIFFRACTION100
2.335-2.42840.1329503775281400.118520858834556X-RAY DIFFRACTION100
2.4284-2.53870.1404165157761470.1190310189024563X-RAY DIFFRACTION100
2.5387-2.67230.1281743983151430.1174051458814578X-RAY DIFFRACTION100
2.6723-2.83930.1340678752691540.1045693456374575X-RAY DIFFRACTION100
2.8393-3.05790.1342483484561390.1099348119384579X-RAY DIFFRACTION100
3.0579-3.36450.1271487677921380.1101165868764576X-RAY DIFFRACTION100
3.3645-3.84860.1042232163071460.1018600715174549X-RAY DIFFRACTION99.5969452694
3.8486-4.83870.1113854028991390.09288607528114512X-RAY DIFFRACTION98.7473460722
4.8387-20.76050.1493387172611380.1482053968424346X-RAY DIFFRACTION94.8593188069

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