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- PDB-6n4z: Tetragonal thermolysin (with 50% xylose) plunge cooled in liquid ... -

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Basic information

Entry
Database: PDB / ID: 6n4z
TitleTetragonal thermolysin (with 50% xylose) plunge cooled in liquid nitrogen to 77 K
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 / 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 / SAD / Resolution: 1.4 Å
AuthorsJuers, D.H. / Harrison, K. / Wu, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM0900248 United States
CitationJournal: J.Appl.Crystallogr. / Year: 2019
Title: A comparison of gas stream cooling and plunge cooling of macromolecular crystals.
Authors: Harrison, K. / Wu, Z. / Juers, D.H.
History
DepositionNov 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 / _struct_conn.ptnr2_symmetry
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)36,29020
Polymers34,3601
Non-polymers1,92919
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.725, 96.725, 106.535
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

#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
#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.: 7 / Source method: obtained synthetically / Formula: Zn
#4: 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.: 9
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 66.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Drop: 75 mg/ml protein in 45% DMSO/0.5 ZnCl2, Well: 1 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.4→29.4 Å / Num. obs: 98771 / % possible obs: 99.2 % / Redundancy: 11.6 % / Biso Wilson estimate: 16.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Net I/σ(I): 20.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.82 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 9449 / CC1/2: 0.277 / Rpim(I) all: 1.03 / Rrim(I) all: 3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CrysalisPro1.14_3260data collection
CrysalisPro1.14_3260data reduction
CrysalisProdata scaling
PHENIXphasing
PHENIX1.14_3260refinement
RefinementMethod to determine structure: SAD / Resolution: 1.4→29.4 Å / SU ML: 0.1676 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.8197
RfactorNum. reflection% reflection
Rfree0.1612 4859 4.92 %
Rwork0.1389 --
obs0.14 98694 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.56 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 100 418 2950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662838
X-RAY DIFFRACTIONf_angle_d0.90283908
X-RAY DIFFRACTIONf_chiral_restr0.0762440
X-RAY DIFFRACTIONf_plane_restr0.0056506
X-RAY DIFFRACTIONf_dihedral_angle_d13.7791015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.4071480.35722923X-RAY DIFFRACTION94.96
1.42-1.430.34031450.31513021X-RAY DIFFRACTION96.23
1.43-1.450.29121500.29292996X-RAY DIFFRACTION96.89
1.45-1.470.31771430.27663084X-RAY DIFFRACTION97.55
1.47-1.490.26651350.25043056X-RAY DIFFRACTION97.49
1.49-1.510.26521550.23453055X-RAY DIFFRACTION98.14
1.51-1.530.25041590.21773065X-RAY DIFFRACTION98.53
1.53-1.550.23041560.20523082X-RAY DIFFRACTION98.84
1.55-1.580.22151740.23089X-RAY DIFFRACTION98.97
1.58-1.60.21681730.1893078X-RAY DIFFRACTION99.24
1.6-1.630.21291430.17743103X-RAY DIFFRACTION99.54
1.63-1.660.21451550.16853129X-RAY DIFFRACTION99.73
1.66-1.690.19692050.16483097X-RAY DIFFRACTION99.79
1.69-1.730.2021760.15253104X-RAY DIFFRACTION100
1.73-1.760.16441540.1373122X-RAY DIFFRACTION100
1.76-1.80.17281550.12713160X-RAY DIFFRACTION100
1.8-1.850.14461350.12763152X-RAY DIFFRACTION100
1.85-1.90.14221490.11873169X-RAY DIFFRACTION99.97
1.9-1.960.15071580.12013131X-RAY DIFFRACTION100
1.96-2.020.1441750.12033135X-RAY DIFFRACTION100
2.02-2.090.16081770.11833144X-RAY DIFFRACTION100
2.09-2.170.13611490.11013169X-RAY DIFFRACTION99.97
2.17-2.270.14231810.10663143X-RAY DIFFRACTION100
2.27-2.390.12731670.10483156X-RAY DIFFRACTION100
2.39-2.540.13051740.11453183X-RAY DIFFRACTION99.94
2.54-2.740.1471580.11023188X-RAY DIFFRACTION99.88
2.74-3.020.13721870.11333179X-RAY DIFFRACTION99.97
3.02-3.450.13481730.12393237X-RAY DIFFRACTION100
3.45-4.350.12721590.11473266X-RAY DIFFRACTION100
4.35-30.590.17291910.173419X-RAY DIFFRACTION99.83

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