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- PDB-3fh2: The crystal structure of the PROBABLE ATP-DEPENDENT PROTEASE (HEA... -

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Basic information

Entry
Database: PDB / ID: 3fh2
TitleThe crystal structure of the PROBABLE ATP-DEPENDENT PROTEASE (HEAT SHOCK PROTEIN) from Corynebacterium glutamicum
ComponentsPROBABLE ATP-DEPENDENT PROTEASE (HEAT SHOCK PROTEIN)
KeywordsHYDROLASE / PROBABLE ATP-DEPENDENT PROTEASE (HEAT SHOCK PROTEIN) / Structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / ATP-binding / Chaperone / Nucleotide-binding / Protease / Stress response
Function / homology
Function and homology information


cellular response to heat / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / Clp amino terminal domain, pathogenicity island component ...Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATPases with chaperone activity, ATP-binding subunit
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Li, H. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the PROBABLE ATP-DEPENDENT PROTEASE (HEAT SHOCK PROTEIN) from Corynebacterium glutamicum
Authors: Zhang, R. / Li, H. / Freeman, L. / Joachimiak, A.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 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: PROBABLE ATP-DEPENDENT PROTEASE (HEAT SHOCK PROTEIN)


Theoretical massNumber of molelcules
Total (without water)16,1101
Polymers16,1101
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.231, 60.830, 68.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROBABLE ATP-DEPENDENT PROTEASE (HEAT SHOCK PROTEIN) / ATPases with chaperone activity / ATP-binding subunit


Mass: 16109.642 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 / Gene: cg2963, Cgl2678, clpC, GI:41326857 / Plasmid: pMCSG156.19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NMA0, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25.5% PEG4000, 0.085M Na Citrate, 0.17M Ammonium acetate, 15% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→34.38 Å / Num. all: 18037 / Num. obs: 17893 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.1
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.69 / Num. unique all: 1374 / % possible all: 91.63

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→34.38 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.558 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23105 971 5.1 %RANDOM
Rwork0.18894 ---
obs0.19109 17893 99.2 %-
all-18037 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.507 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2---1.3 Å20 Å2
3---2.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 0 131 1261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221144
X-RAY DIFFRACTIONr_bond_other_d0.0020.02794
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9821539
X-RAY DIFFRACTIONr_angle_other_deg1.08331935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66723.65452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7271511
X-RAY DIFFRACTIONr_chiral_restr0.1110.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02223
X-RAY DIFFRACTIONr_mcbond_it1.1181.5717
X-RAY DIFFRACTIONr_mcbond_other0.3711.5303
X-RAY DIFFRACTIONr_mcangle_it1.80321145
X-RAY DIFFRACTIONr_scbond_it3.3853427
X-RAY DIFFRACTIONr_scangle_it5.3994.5394
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 63 -
Rwork0.303 1196 -
obs-1259 91.63 %
Refinement TLS params.Method: refined / Origin x: 30.812 Å / Origin y: 3.579 Å / Origin z: 14.673 Å
111213212223313233
T0.1001 Å2-0.0153 Å20.0085 Å2-0.095 Å20.0038 Å2--0.0036 Å2
L1.1042 °2-0.6455 °2-0.2455 °2-2.3391 °20.3198 °2--0.4785 °2
S-0.0168 Å °0.0023 Å °-0.0033 Å °0.0216 Å °0.0174 Å °0.0724 Å °0.0217 Å °-0.0159 Å °-0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 30
2X-RAY DIFFRACTION1A31 - 60
3X-RAY DIFFRACTION1A61 - 90
4X-RAY DIFFRACTION1A91 - 120
5X-RAY DIFFRACTION1A121 - 144

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