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- PDB-5ycq: Unique Specificity-Enhancing Factor for the AAA+ Lon Protease -

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Basic information

Entry
Database: PDB / ID: 5ycq
TitleUnique Specificity-Enhancing Factor for the AAA+ Lon Protease
ComponentsHeat shock protein HspQ
KeywordsDNA BINDING PROTEIN / heat shock protein
Function / homology
Function and homology information


response to heat / DNA binding / cytoplasm
Similarity search - Function
Hemimethylated DNA-binding domain / Heat shock protein HspQ / Hemimethylated DNA-binding domain / Hemimethylated DNA-binding domain superfamily / Hemimethylated DNA-binding protein YccV like / Hemimethylated DNA-binding protein YccV like / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Heat shock protein HspQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.503 Å
AuthorsAbe, Y. / Shioi, S. / Kita, S. / Nakata, H. / Maenaka, K. / Kohda, D. / Katayama, T. / Ueda, T.
CitationJournal: FEBS Lett. / Year: 2017
Title: X-ray crystal structure of Escherichia coli HspQ, a protein involved in the retardation of replication initiation
Authors: Abe, Y. / Shioi, S. / Kita, S. / Nakata, H. / Maenaka, K. / Kohda, D. / Katayama, T. / Ueda, T.
History
DepositionSep 8, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 11, 2018ID: 1VBV
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Heat shock protein HspQ


Theoretical massNumber of molelcules
Total (without water)11,9311
Polymers11,9311
Non-polymers00
Water1086
1
A: Heat shock protein HspQ

A: Heat shock protein HspQ

A: Heat shock protein HspQ


Theoretical massNumber of molelcules
Total (without water)35,7923
Polymers35,7923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area3370 Å2
ΔGint-20 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.822, 76.822, 85.888
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Heat shock protein HspQ


Mass: 11930.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain 55989 / EAEC) (bacteria)
Strain: 55989 / EAEC / Gene: hspQ, EC55989_1015 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7LE66
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: Ammonium Sulfate, HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9792, 0.9794, 0.9851
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.98511
ReflectionResolution: 2.5→38.41 Å / Num. obs: 3504 / % possible obs: 99.9 % / Redundancy: 20.9 % / Net I/σ(I): 34.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 18.5 % / Mean I/σ(I) obs: 9.03 / Num. unique obs: 337 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.503→38.41 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.65
RfactorNum. reflection% reflection
Rfree0.2655 317 9.07 %
Rwork0.2229 --
obs0.2264 3496 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.503→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms603 0 0 6 609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007616
X-RAY DIFFRACTIONf_angle_d0.831838
X-RAY DIFFRACTIONf_dihedral_angle_d15.551225
X-RAY DIFFRACTIONf_chiral_restr0.03693
X-RAY DIFFRACTIONf_plane_restr0.005111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5028-3.1530.33711610.28081551X-RAY DIFFRACTION100
3.153-38.41550.23911560.20371628X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3972-0.619-2.23473.6761.74.74510.184-0.03080.72150.18480.1944-0.5832-0.3869-0.1567-0.32870.4293-0.00220.00460.51770.00290.384752.474329.0122.9665
28.217-1.77241.56886.1328-3.57142.2798-0.37311.23940.4201-0.38810.50310.0116-1.1355-0.4086-0.23770.6580.0019-0.06260.6574-0.01240.354147.902129.8776-4.8464
38.31811.5839-0.59089.7147-1.50442.911-0.38620.34940.74130.8259-0.0833-0.5558-0.73560.00060.72640.3570.0465-0.06240.37050.00380.500646.119126.84290.5681
43.24561.69840.88998.4-1.41143.98180.1908-0.51810.66310.8915-0.09770.437-0.2644-0.0153-0.16510.2998-0.0194-0.01280.3946-0.00830.510345.660526.71694.6909
56.5217-3.73873.1762.524-9.175910.2370.1492-0.57510.26661.114-0.7733-0.4038-0.29640.74810.81170.6406-0.0054-0.07580.6146-0.02730.627358.718519.27998.6364
610.7838-0.1307-3.82049.13772.24272.6358-0.81530.3914-2.2333-0.4936-0.3243-0.1823-0.3136-0.42780.72880.54610.0774-0.01570.51870.03360.768254.052715.4707-1.529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 75 )
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 84 )
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 97 )

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