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- PDB-5uue: Tetragonal thermolysin cryocooled to 100 K with 50% methanol as c... -

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Basic information

Entry
Database: PDB / ID: 5uue
TitleTetragonal thermolysin cryocooled to 100 K with 50% methanol 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
METHANOL / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.60000115572 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_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_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)35,27122
Polymers34,3601
Non-polymers91121
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-289 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.149, 96.149, 104.800
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 , 5 types, 428 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.: 6 / 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-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 3.52 Å3/Da / Density % sol: 65.1 %
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: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→20.801 Å / Num. obs: 121775 / % possible obs: 98.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.5712077884 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.1
Reflection shellHighest resolution: 1.6 Å / Redundancy: 4.9 % / CC1/2: 0.178 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CrysalisProdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.60000115572→20.8005965727 Å / SU ML: 0.257288165086 / Cross valid method: FREE R-VALUE / σ(F): 0.901022574281 / Phase error: 26.7832114386
RfactorNum. reflection% reflection
Rfree0.234896015388 3653 3.00107621403 %
Rwork0.201233500558 --
obs0.202239463246 121723 98.3143526371 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.8586592548 Å2
Refinement stepCycle: LAST / Resolution: 1.60000115572→20.8005965727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 29 407 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009465184029982570
X-RAY DIFFRACTIONf_angle_d0.9460401620063509
X-RAY DIFFRACTIONf_chiral_restr0.0579358727924375
X-RAY DIFFRACTIONf_plane_restr0.00655499663809465
X-RAY DIFFRACTIONf_dihedral_angle_d9.848119969981490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6210.391981110521120.3936536897994172X-RAY DIFFRACTION90.3797468354
1.621-1.64320.4220941358431430.3851368970914257X-RAY DIFFRACTION92.7487352445
1.6432-1.66670.3953048167581260.3758140421154396X-RAY DIFFRACTION94.110301769
1.6667-1.69160.3914401302661220.3598810606474399X-RAY DIFFRACTION95.2591656131
1.6916-1.7180.4109633692871410.3537937425384444X-RAY DIFFRACTION95.6204379562
1.718-1.74610.3627884357651290.3520584887814459X-RAY DIFFRACTION96.447340761
1.7461-1.77620.4112452658131500.3319405525394497X-RAY DIFFRACTION97.4418117006
1.7762-1.80850.3191005912911290.3270374740434515X-RAY DIFFRACTION97.9953576704
1.8085-1.84330.2816593476611450.3134534930344560X-RAY DIFFRACTION98.6373165618
1.8433-1.88090.3262788609411610.2945190530544558X-RAY DIFFRACTION99.0970180596
1.8809-1.92180.3121336019821350.2750616246014623X-RAY DIFFRACTION99.6857322439
1.9218-1.96640.2942246344531380.265849763974599X-RAY DIFFRACTION99.9367088608
1.9664-2.01560.2727261714841530.2577383836484607X-RAY DIFFRACTION99.9370144867
2.0156-2.070.2839906881231350.2412541407674609X-RAY DIFFRACTION99.9368021909
2.07-2.13090.2205133840221440.2176094057634634X-RAY DIFFRACTION99.7286579002
2.1309-2.19960.2412943233951470.2160191477614572X-RAY DIFFRACTION99.8941574936
2.1996-2.27810.2516316705111440.1995362955134646X-RAY DIFFRACTION99.958263773
2.2781-2.36920.19828691971420.1802818743814591X-RAY DIFFRACTION100
2.3692-2.47690.2600361416151340.1821236454834618X-RAY DIFFRACTION99.9789606564
2.4769-2.60720.2044407567081530.165440884614629X-RAY DIFFRACTION100
2.6072-2.77020.1745059124911560.1613460698664621X-RAY DIFFRACTION99.9790707409
2.7702-2.98350.2382390508831440.1770078715814588X-RAY DIFFRACTION100
2.9835-3.28270.2220733648321370.1827327581784623X-RAY DIFFRACTION100
3.2827-3.75530.2164824205381420.1632711688354629X-RAY DIFFRACTION100
3.7553-4.72220.1896044280691450.1309744083234623X-RAY DIFFRACTION100
4.7222-20.80230.1548627676241460.1467864849124601X-RAY DIFFRACTION99.5178197065

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