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- PDB-5un3: Tetragonal thermolysin (295 K) in the presence of 50% xylose -

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Basic information

Entry
Database: PDB / ID: 5un3
TitleTetragonal thermolysin (295 K) in the presence of 50% xylose
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 / MOLECULAR REPLACEMENT / Resolution: 1.60004437941 Å
AuthorsJuers, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R15GM090248-02 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
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Other
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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 1.4Jan 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_dist_value / _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_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 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)35,89621
Polymers34,3601
Non-polymers1,53620
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-362 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.659, 97.659, 108.069
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, 6 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


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 5
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, 260 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.: 8 / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Drop: 45% DMSO, 0.5 M ZnCl2, 50 mg/mL protein Well: ~2 M AmSO4

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Oct 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→20.2 Å / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 17.8881911535 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.7 % / CC1/2: 0.258 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
CrysalisPro1.171.37.34data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.60004437941→20.2103390027 Å / SU ML: 0.206163723556 / Cross valid method: FREE R-VALUE / σ(F): 0.599035467022 / Phase error: 21.2053246406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.181278229297 3661 3.01612278693 %
Rwork0.161064848659 117720 -
obs0.161675976423 121381 92.1696673324 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9817184503 Å2
Refinement stepCycle: LAST / Resolution: 1.60004437941→20.2103390027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 65 245 2742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007098054898852634
X-RAY DIFFRACTIONf_angle_d0.8851633129913610
X-RAY DIFFRACTIONf_chiral_restr0.0538427923348399
X-RAY DIFFRACTIONf_plane_restr0.00585083125188469
X-RAY DIFFRACTIONf_dihedral_angle_d9.744040772271508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62110.3738784776581360.3596949146544040X-RAY DIFFRACTION83.1044776119
1.6211-1.64330.391968539031270.3603414249054243X-RAY DIFFRACTION86.0066915961
1.6433-1.66680.3940951837951370.3529802876064267X-RAY DIFFRACTION86.6076696165
1.6668-1.69160.36988975481240.3333462854334266X-RAY DIFFRACTION86.5877712032
1.6916-1.7180.3617488934361270.3359069150374295X-RAY DIFFRACTION86.9958685815
1.718-1.74620.3523990012591350.3163536948414249X-RAY DIFFRACTION86.9496231654
1.7462-1.77630.2955085578881260.2979311944984327X-RAY DIFFRACTION87.2966085081
1.7763-1.80860.270221739131310.283622477294268X-RAY DIFFRACTION87.5945838311
1.8086-1.84330.310388895481340.2619291038514321X-RAY DIFFRACTION87.5245579568
1.8433-1.88090.2432142722091370.24222943144292X-RAY DIFFRACTION87.9118697896
1.8809-1.92180.1990388456461390.2225301471444321X-RAY DIFFRACTION87.6400078601
1.9218-1.96650.2156023711081290.2013913430394317X-RAY DIFFRACTION87.9873342569
1.9665-2.01560.2465099399641280.1996250036274322X-RAY DIFFRACTION88.0142405063
2.0156-2.070.2057896273251370.1795709813254350X-RAY DIFFRACTION88.7284951552
2.07-2.13090.1700778450441430.1675008520094425X-RAY DIFFRACTION90.3302353174
2.1309-2.19960.1842295477081420.1651458670234667X-RAY DIFFRACTION94.9269640742
2.1996-2.27810.1896416972471490.1457714574914794X-RAY DIFFRACTION96.7318982387
2.2781-2.36920.1460028061731580.1363971687394804X-RAY DIFFRACTION98.2574257426
2.3692-2.47680.1739057620151420.1352625310634850X-RAY DIFFRACTION98.7927963586
2.4768-2.60720.1463288943631560.1301260911434866X-RAY DIFFRACTION99.3078900534
2.6072-2.77010.1471995665271620.1172222000614907X-RAY DIFFRACTION99.704956727
2.7701-2.98340.1422514201461530.1144897792984914X-RAY DIFFRACTION99.9802683504
2.9834-3.28250.1465797899371520.1210248095674893X-RAY DIFFRACTION100
3.2825-3.75480.1217670286981470.1063909214944X-RAY DIFFRACTION100
3.7548-4.72070.1151574909421580.09937308235094900X-RAY DIFFRACTION100
4.7207-20.21190.174087799391520.1595989148294878X-RAY DIFFRACTION99.3678387989

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