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- PDB-5uu9: Tetragonal thermolysin cryocooled to 100 K with 40% xylose as cry... -

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Basic information

Entry
Database: PDB / ID: 5uu9
TitleTetragonal thermolysin cryocooled to 100 K with 40% xylose 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
beta-D-xylopyranose / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.59969199601 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,02117
Polymers34,3601
Non-polymers1,66116
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-197 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.819, 96.819, 106.900
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 / Sugars , 2 types, 9 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
#4: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 424 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.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 416 / 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: 3.65 Å3/Da / Density % sol: 66.26 %
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: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.599→20.99 Å / Num. obs: 125129 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.4176084655 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellHighest resolution: 1.6 Å / Redundancy: 2.7 % / CC1/2: 0.671 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIXphasing
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.59969199601→20.987595795 Å / SU ML: 0.16282937592 / Cross valid method: FREE R-VALUE / σ(F): 1.33646126926 / Phase error: 18.0231451875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.177722430154 3770 3.01407099456 %
Rwork0.159168132997 121310 -
obs0.159721636871 125080 97.6104633922 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.7834822726 Å2
Refinement stepCycle: LAST / Resolution: 1.59969199601→20.987595795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 91 416 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008548796725092736
X-RAY DIFFRACTIONf_angle_d0.9666092692693765
X-RAY DIFFRACTIONf_chiral_restr0.0554111783313425
X-RAY DIFFRACTIONf_plane_restr0.00604216202448485
X-RAY DIFFRACTIONf_dihedral_angle_d9.93177921731586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5997-1.61990.3109991532611260.3156059730974215X-RAY DIFFRACTION90.8539137715
1.6199-1.64120.2941690032011360.2925416038084300X-RAY DIFFRACTION93.5667580679
1.6412-1.66370.3341539716511320.2961224542064334X-RAY DIFFRACTION94.3986472205
1.6637-1.68750.3061686364161370.2744803735784371X-RAY DIFFRACTION95.2864087931
1.6875-1.71270.2574809112781360.2642449564124465X-RAY DIFFRACTION96.7206222409
1.7127-1.73940.2799133188711450.2619131193534485X-RAY DIFFRACTION97.5558364939
1.7394-1.76790.2125347576331380.2510654598774480X-RAY DIFFRACTION98.2553191489
1.7679-1.79840.2209685864981420.2309382652294577X-RAY DIFFRACTION98.5794861082
1.7984-1.83110.2485843480391400.2131934910074542X-RAY DIFFRACTION98.6722866175
1.8311-1.86630.2066506686111410.2065948183994560X-RAY DIFFRACTION98.8020176545
1.8663-1.90430.1971389824961460.1944550067764568X-RAY DIFFRACTION98.9089383131
1.9043-1.94570.2286066302341400.1774793882034506X-RAY DIFFRACTION98.8721004469
1.9457-1.99090.1879244428321390.1831366242034539X-RAY DIFFRACTION98.921547896
1.9909-2.04070.1726741766931480.1693522312764573X-RAY DIFFRACTION98.9934996855
2.0407-2.09580.2092411053631470.1646454455644557X-RAY DIFFRACTION98.927444795
2.0958-2.15740.200653495231380.1585299388574541X-RAY DIFFRACTION98.9636209814
2.1574-2.2270.174981908731410.1455334742724585X-RAY DIFFRACTION98.9738219895
2.227-2.30650.1386301041241400.1316977150714533X-RAY DIFFRACTION98.7949260042
2.3065-2.39870.1381666977031380.124976091524522X-RAY DIFFRACTION98.4784446323
2.3987-2.50770.1432995345241390.126145878374486X-RAY DIFFRACTION97.8008035525
2.5077-2.63970.1518240882021410.1223217561894467X-RAY DIFFRACTION96.8067226891
2.6397-2.80470.118141452911380.1190129555434435X-RAY DIFFRACTION96.2939566224
2.8047-3.02070.1480348923951380.1286398098964472X-RAY DIFFRACTION96.8894493485
3.0207-3.32360.1911318362511370.1390706804664548X-RAY DIFFRACTION98.7979755377
3.3236-3.8020.1361559461411410.1311125949694568X-RAY DIFFRACTION99.0951178451
3.802-4.78080.1353716866531420.1173489916494569X-RAY DIFFRACTION99.4511294068
4.7808-20.98940.1878068921331440.1649356564694512X-RAY DIFFRACTION97.897392767

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