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- PDB-5wsl: Structural studies of keratinase from Meiothermus taiwanensis WR-220 -

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Basic information

Entry
Database: PDB / ID: 5wsl
TitleStructural studies of keratinase from Meiothermus taiwanensis WR-220
Componentskeratinase
KeywordsHYDROLASE / keratainase / protease
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMeiothermus taiwanensis WR-220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHo, M.C. / Wu, S.H. / Chen, M.Y. / Tu, I.F.
CitationJournal: Sci Rep / Year: 2017
Title: The discovery of novel heat-stable keratinases from Meiothermus taiwanensis WR-220 and other extremophiles
Authors: Wu, W.L. / Chen, M.Y. / Tu, I.F. / Lin, Y.C. / EswarKumar, N. / Chen, M.Y. / Ho, M.C. / Wu, S.H.
History
DepositionDec 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_auth_asym_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: keratinase
B: keratinase
C: keratinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,50118
Polymers92,3963
Non-polymers1,10515
Water11,890660
1
A: keratinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2637
Polymers30,7991
Non-polymers4646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10300 Å2
MethodPISA
2
B: keratinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2637
Polymers30,7991
Non-polymers4646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area10280 Å2
MethodPISA
3
C: keratinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9754
Polymers30,7991
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.210, 67.088, 92.857
Angle α, β, γ (deg.)90.000, 96.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein keratinase


Mass: 30798.643 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis WR-220 (bacteria)
Strain: WR-220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4A2Y5*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M lithium sulfate, 0.1M sodium acetate, 50% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 115261 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rsym value: 0.012 / Net I/σ(I): 10.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZT

4dzt


Resolution: 1.5→25.23 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.336 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1754 5617 5 %RANDOM
Rwork0.145 ---
obs0.1466 106459 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.08 Å2 / Biso mean: 12.966 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.06 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.5→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 51 660 6732
Biso mean--22.12 25.99 -
Num. residues----846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0196233
X-RAY DIFFRACTIONr_bond_other_d0.0030.025645
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.9258531
X-RAY DIFFRACTIONr_angle_other_deg1.157312887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67623.457243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78915839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1931545
X-RAY DIFFRACTIONr_chiral_restr0.1370.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021503
LS refinement shellResolution: 1.502→1.541 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 398 -
Rwork0.198 7575 -
all-7973 -
obs--94.03 %

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