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- PDB-2z3b: Crystal Structure of Bacillus Subtilis CodW, a non-canonical HslV... -

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Basic information

Entry
Database: PDB / ID: 2z3b
TitleCrystal Structure of Bacillus Subtilis CodW, a non-canonical HslV-like peptidase with an impaired catalytic apparatus
ComponentsATP-dependent protease hslV
KeywordsHYDROLASE / N-terminal nucleophile 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
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: 2.5 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,74224
Polymers232,46612
Non-polymers27612
Water4,522251
1
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,74224
Polymers232,46612
Non-polymers27612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area37030 Å2
ΔGint-316.9 kcal/mol
Surface area72500 Å2
MethodPISA
2
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,74224
Polymers232,46612
Non-polymers27612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area36880 Å2
ΔGint-329.3 kcal/mol
Surface area73650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.050, 106.800, 152.700
Angle α, β, γ (deg.)90.00, 112.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12G
22H
32I
42J
52K
62L

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 1 - 180 / Label seq-ID: 1 - 180

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
31CC
41DD
51EE
61FF
12GG
22HH
32II
42JJ
52KK
62LL

NCS ensembles :
ID
1
2

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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) / Gene: CODW / Production host: Escherichia coli (E. coli)
References: UniProt: P39070, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: NA HEPES, NA CITRATE, pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 / Wavelength: 1.12714 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 27, 2001 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 90904 / Num. obs: 90904 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.055 / Net I/σ(I): 17.2
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 2.76 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.88 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.403 / SU ML: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.531 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4576 5 %RANDOM
Rwork0.226 ---
all0.228 86652 --
obs0.228 86652 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.06 Å2
2--0 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16308 0 12 251 16571
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.528
X-RAY DIFFRACTIONr_angle_other_deg2.061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.417
X-RAY DIFFRACTIONr_chiral_restr
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1061medium positional0.170.5
12B1061medium positional0.320.5
13C1061medium positional0.210.5
14D1061medium positional0.230.5
15E1061medium positional0.320.5
16F1061medium positional0.230.5
21G1061medium positional0.220.5
22H1061medium positional0.260.5
23I1061medium positional0.210.5
24J1061medium positional0.240.5
25K1061medium positional0.250.5
26L1061medium positional0.250.5
11A1583loose positional0.365
12B1583loose positional0.665
13C1583loose positional0.435
14D1583loose positional0.55
15E1583loose positional0.465
16F1583loose positional0.395
21G1583loose positional0.45
22H1583loose positional0.655
23I1583loose positional0.45
24J1583loose positional0.415
25K1583loose positional0.45
26L1583loose positional0.415
11A1061medium thermal0.842
12B1061medium thermal1.032
13C1061medium thermal1.022
14D1061medium thermal1.192
15E1061medium thermal1.052
16F1061medium thermal0.992
21G1061medium thermal0.862
22H1061medium thermal0.872
23I1061medium thermal0.832
24J1061medium thermal0.92
25K1061medium thermal0.872
26L1061medium thermal1.042
11A1583loose thermal1.0710
12B1583loose thermal1.3910
13C1583loose thermal1.3510
14D1583loose thermal1.3310
15E1583loose thermal1.4310
16F1583loose thermal1.2410
21G1583loose thermal1.0310
22H1583loose thermal1.0810
23I1583loose thermal1.0510
24J1583loose thermal1.1510
25K1583loose thermal1.1410
26L1583loose thermal1.2110
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 289
Rwork0.336 5768

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