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- PDB-6d5r: Hexagonal thermolysin cryocooled to 100 K with 50% xylose as cryo... -

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Basic information

Entry
Database: PDB / ID: 6d5r
TitleHexagonal thermolysin cryocooled to 100 K with 50% xylose as cryoprotectant
ComponentsThermolysin
KeywordsHYDROLASE / zinc protease
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
LYSINE / VALINE / beta-D-xylopyranose / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.00002117296 Å
AuthorsJuers, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R15GM090248 United States
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
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_value_order / _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.ptnr1_label_seq_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 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)35,45112
Polymers34,3601
Non-polymers1,09111
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.920, 92.920, 130.122
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-732-

HOH

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin
#6: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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 , 5 types, 300 molecules

#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Protein: 100 mg/mL in 45% DMSO Well: 2 M AmSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→13.81 Å / Num. obs: 23018 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 16.065813782 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.104 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.11 Å / Mean I/σ(I) obs: 4.7 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHENIX1.10.1_2155refinement
SCALAdata scaling
RefinementResolution: 2.00002117296→13.805000825 Å / SU ML: 0.18392565931 / Cross valid method: FREE R-VALUE / σ(F): 1.34352131225 / Phase error: 18.8497856914
RfactorNum. reflection% reflection
Rfree0.204626731152 1086 4.72831765935 %
Rwork0.153888020084 --
obs0.156280395524 22968 99.9390827604 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.5538153163 Å2
Refinement stepCycle: LAST / Resolution: 2.00002117296→13.805000825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 45 293 2787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233328725352635
X-RAY DIFFRACTIONf_angle_d0.5453337745293606
X-RAY DIFFRACTIONf_chiral_restr0.0417257803546393
X-RAY DIFFRACTIONf_plane_restr0.00247523445968475
X-RAY DIFFRACTIONf_dihedral_angle_d9.697418651491516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.09080.23313386441170.1849553642942690X-RAY DIFFRACTION99.9643874644
2.0908-2.20060.2227183588281310.1640426103612674X-RAY DIFFRACTION99.9643620813
2.2006-2.33780.2115803311971480.1528154289162670X-RAY DIFFRACTION100
2.3378-2.51730.2043632355921500.148657435182686X-RAY DIFFRACTION100
2.5173-2.76880.238873191661300.1511997662192715X-RAY DIFFRACTION99.9648629656
2.7688-3.16520.1902559018591230.1577151699862748X-RAY DIFFRACTION100
3.1652-3.97210.2237255370151390.1417110598212783X-RAY DIFFRACTION100
3.9721-13.80530.1668791704171480.1533494578462916X-RAY DIFFRACTION99.6422764228

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