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- PDB-5uua: Tetragonal thermolysin cryocooled to 100 K with 50% xylose as cry... -

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Basic information

Entry
Database: PDB / ID: 5uua
TitleTetragonal thermolysin cryocooled to 100 K with 50% 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 / Thermolysin metallopeptidase, alpha-helical 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 / MOLECULAR REPLACEMENT / Resolution: 1.60000384919 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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_atom_id_1 / _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_label_asym_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)36,30723
Polymers34,3601
Non-polymers1,94622
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-363 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.705, 96.705, 106.734
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
#5: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / 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, 475 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Protein: 50 mg/mL in 45% DMSO, 0.5 M ZnC2

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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 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→21.2 Å / Num. obs: 127553 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 15.3600259248 Å2 / CC1/2: 0.999 / Net I/σ(I): 29.3
Reflection shellHighest resolution: 1.6 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.734 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALAdata scaling
CrysalisProdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.60000384919→21.0355652469 Å / SU ML: 0.145654428223 / Cross valid method: FREE R-VALUE / σ(F): 1.34439842831 / Phase error: 16.0668765575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.166000093328 3844 3.01431091943 %
Rwork0.144735730355 123681 -
obs0.145369092285 127525 99.9772645311 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.9942011237 Å2
Refinement stepCycle: LAST / Resolution: 1.60000384919→21.0355652469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 94 461 2987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01030274661562732
X-RAY DIFFRACTIONf_angle_d1.078052496753758
X-RAY DIFFRACTIONf_chiral_restr0.061732078158424
X-RAY DIFFRACTIONf_plane_restr0.00705451933052484
X-RAY DIFFRACTIONf_dihedral_angle_d9.845676102881585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62020.2947830000731400.27765881264595X-RAY DIFFRACTION99.9366821444
1.6202-1.64160.2672116047431420.261058335834548X-RAY DIFFRACTION99.9786825837
1.6416-1.6640.3052366158911410.2512905691054614X-RAY DIFFRACTION100
1.664-1.68780.2546014836731420.2342486266614590X-RAY DIFFRACTION100
1.6878-1.7130.2300155264221450.2237430664454551X-RAY DIFFRACTION100
1.713-1.73970.2264839791441430.2151807085054589X-RAY DIFFRACTION100
1.7397-1.76820.1924255094881420.2085979350064575X-RAY DIFFRACTION100
1.7682-1.79870.1962548171461430.1918778158944617X-RAY DIFFRACTION100
1.7987-1.83140.2074580215531400.1811654336564556X-RAY DIFFRACTION100
1.8314-1.86660.1943305162691420.1716266914124583X-RAY DIFFRACTION100
1.8666-1.90470.1711301951271490.1671272414974577X-RAY DIFFRACTION100
1.9047-1.94610.1900668295441420.1548921431224606X-RAY DIFFRACTION100
1.9461-1.99130.1602261208381410.154747099424521X-RAY DIFFRACTION100
1.9913-2.04110.1684271780741450.1515096716424640X-RAY DIFFRACTION100
2.0411-2.09620.1960511141231470.1492107775454553X-RAY DIFFRACTION100
2.0962-2.15780.2078568322141360.1438137292964576X-RAY DIFFRACTION100
2.1578-2.22740.1675235514791430.1347039662944563X-RAY DIFFRACTION100
2.2274-2.30690.1251850068931420.1238575595444610X-RAY DIFFRACTION100
2.3069-2.39920.1287685311311390.1184707256514588X-RAY DIFFRACTION100
2.3992-2.50820.1473599082351440.1235219199294569X-RAY DIFFRACTION100
2.5082-2.64020.1182912194711420.1154682575984579X-RAY DIFFRACTION100
2.6402-2.80530.1145990482911470.1116004623014596X-RAY DIFFRACTION100
2.8053-3.02130.1270780491861370.1173121304114574X-RAY DIFFRACTION100
3.0213-3.32420.1796840356571410.1278826668144585X-RAY DIFFRACTION100
3.3242-3.80280.1266398404341420.1219048981064584X-RAY DIFFRACTION100
3.8028-4.78180.1416377837021440.1111711536424585X-RAY DIFFRACTION100
4.7818-21.03740.2023887390591430.1640944815294557X-RAY DIFFRACTION99.4708994709

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