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- PDB-2z3a: Crystal Structure of Bacillus Subtilis CodW, a non-canonical HslV... -

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Basic information

Entry
Database: PDB / ID: 2z3a
TitleCrystal Structure of Bacillus Subtilis CodW, a non-canonical HslV-like peptidase with an impaired catalytic apparatus
ComponentsATP-dependent protease hslV
KeywordsHYDROLASE / ATP-dependent protease / NTN-hydrolase
Function / homology
Function and homology information


HslUV protease complex / proteasome core complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / threonine-type endopeptidase activity / serine-type peptidase activity / proteolysis involved in protein catabolic process / metal ion binding / cytoplasm
Similarity search - Function
ATP-dependent protease, HslV subunit / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent protease subunit ClpQ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRho, S.H. / Park, H.H. / Kang, G.B. / Lim, Y.J. / Kang, M.S. / Lim, B.K. / Seong, I.S. / Chung, C.H. / Wang, J. / Eom, S.H.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of Bacillus subtilis CodW, a noncanonical HslV-like peptidase with an impaired catalytic apparatus
Authors: Rho, S.H. / Park, H.H. / Kang, G.B. / Im, Y.J. / Kang, M.S. / Lim, B.K. / Seong, I.S. / Seol, J. / Chung, C.H. / Wang, J. / Eom, S.H.
History
DepositionJun 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent protease hslV
B: ATP-dependent protease hslV
C: ATP-dependent protease hslV
D: ATP-dependent protease hslV
E: ATP-dependent protease hslV
F: ATP-dependent protease hslV
G: ATP-dependent protease hslV
H: ATP-dependent protease hslV
I: ATP-dependent protease hslV
J: ATP-dependent protease hslV
K: ATP-dependent protease hslV
L: ATP-dependent protease hslV


Theoretical massNumber of molelcules
Total (without water)232,46612
Polymers232,46612
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32790 Å2
ΔGint-169 kcal/mol
Surface area70660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.130, 164.420, 95.900
Angle α, β, γ (deg.)90.00, 111.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ATP-dependent protease hslV / ATP-DEPENDENT PROTEASE CODW


Mass: 19372.135 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P39070, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.45 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MPD, SODIUM CITRATE, GLYCEROL, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.127 / Wavelength: 1.127 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 26, 2002
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 3→45 Å / Num. all: 44182 / Num. obs: 44150 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.117 / Rsym value: 0.089 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.16 Å / % possible all: 97.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→40.37 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1581367.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4438 10.1 %RANDOM
Rwork0.245 ---
all0.247 44182 --
obs0.247 44150 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.43 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å24.09 Å2
2---1.1 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16308 0 0 106 16414
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 747 10.2 %
Rwork0.34 6589 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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