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- PDB-5uuc: Tetragonal thermolysin cryocooled to 100 K with 50% mpd as cryopr... -

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Basic information

Entry
Database: PDB / ID: 5uuc
TitleTetragonal thermolysin cryocooled to 100 K with 50% mpd as cryoprotectant
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: 1.60000931163 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_symmetry / _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.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.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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,95624
Polymers34,3601
Non-polymers1,59523
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-419 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.546, 96.546, 105.280
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 , 6 types, 414 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.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Well: 2 M AmSO4 Drop: 50 mg/mL protein in 45% DMSO, 0.5 M ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→20.89 Å / Num. obs: 125186 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 15.7313800319 Å2 / CC1/2: 1 / Net I/σ(I): 27.6
Reflection shellHighest resolution: 1.6 Å / CC1/2: 0.752 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CrysalisProdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.60000931163→19.8868861009 Å / SU ML: 0.140938768952 / Cross valid method: FREE R-VALUE / σ(F): 1.33649007349 / Phase error: 15.9525160569
RfactorNum. reflection% reflection
Rfree0.166069619311 3778 3.01875334596 %
Rwork0.140975610198 --
obs0.141741795682 125151 99.7887031958 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.2290579878 Å2
Refinement stepCycle: LAST / Resolution: 1.60000931163→19.8868861009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 65 391 2888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01566828874952641
X-RAY DIFFRACTIONf_angle_d1.297987980843625
X-RAY DIFFRACTIONf_chiral_restr0.077763880417388
X-RAY DIFFRACTIONf_plane_restr0.0100903677134473
X-RAY DIFFRACTIONf_dihedral_angle_d10.92898851631534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62030.264630652531400.2645941293964519X-RAY DIFFRACTION99.4450373533
1.6203-1.64160.2910116782081300.2568014403484510X-RAY DIFFRACTION99.8708566509
1.6416-1.6640.2373024865161450.2386528988274472X-RAY DIFFRACTION99.7192224622
1.664-1.68780.2344019889151350.2279709852054471X-RAY DIFFRACTION99.5676610463
1.6878-1.7130.193890577121410.2148965968534443X-RAY DIFFRACTION99.5439739414
1.713-1.73970.2492587837171470.2008365317384517X-RAY DIFFRACTION99.4244297591
1.7397-1.76820.2016530925271440.1996459616834451X-RAY DIFFRACTION99.3728373702
1.7682-1.79870.2035235061631340.1930595799164484X-RAY DIFFRACTION99.2691315563
1.7987-1.83140.2216546150141430.182575347134482X-RAY DIFFRACTION99.2489270386
1.8314-1.86660.2189266044191310.1721501303884482X-RAY DIFFRACTION99.6113150507
1.8666-1.90470.1930209522261590.1693858074074471X-RAY DIFFRACTION99.8921251348
1.9047-1.9460.2205517479321350.1606821760284530X-RAY DIFFRACTION100
1.946-1.99130.1904109332291330.1525726976264496X-RAY DIFFRACTION100
1.9913-2.0410.2095176613551460.1574369097454504X-RAY DIFFRACTION100
2.041-2.09610.1539321124911430.1528252228044508X-RAY DIFFRACTION100
2.0961-2.15780.202209576621370.1381236229314512X-RAY DIFFRACTION100
2.1578-2.22730.1472410274611460.1242983355434496X-RAY DIFFRACTION100
2.2273-2.30680.1434299306041340.1237004932694510X-RAY DIFFRACTION100
2.3068-2.3990.1375670929861330.1132808584374511X-RAY DIFFRACTION100
2.399-2.5080.1481271470761410.1159357255514487X-RAY DIFFRACTION100
2.508-2.640.1301290736151420.115364016844505X-RAY DIFFRACTION100
2.64-2.80490.1388234701921440.1044808759844507X-RAY DIFFRACTION100
2.8049-3.02080.1161496248811410.1091644424814510X-RAY DIFFRACTION100
3.0208-3.32350.1562852218031370.1166303788614525X-RAY DIFFRACTION100
3.3235-3.80160.118600580951390.1136138709674486X-RAY DIFFRACTION100
3.8016-4.77860.1621816683091380.1151195716894514X-RAY DIFFRACTION100
4.7786-19.88840.1731475659921400.1643428830924470X-RAY DIFFRACTION99.3320405085

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