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- PDB-5zzo: Crystal structure of CcpE regulatory domain in complex with citra... -

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Basic information

Entry
Database: PDB / ID: 5zzo
TitleCrystal structure of CcpE regulatory domain in complex with citrate from Staphyloccocus aureus
ComponentsLysR family transcriptional regulator
KeywordsTRANSCRIPTION / citrate-bound / Staphyloccocus aureus / transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Hydrogen peroxide-inducible genes activator / Hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, J. / Wang, L. / Shang, F. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31200556 China
National Natural Science Foundation of China21272031 China
CitationJournal: Biochemistry / Year: 2018
Title: Structural and Biochemical Analysis of the Citrate-Responsive Mechanism of the Regulatory Domain of Catabolite Control Protein E from Staphylococcus aureus
Authors: Chen, J. / Shang, F. / Wang, L. / Zou, L. / Bu, T. / Jin, L. / Dong, Y. / Ha, N.C. / Quan, C. / Nam, K.H. / Xu, Y.
History
DepositionJun 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: LysR family transcriptional regulator
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
D: LysR family transcriptional regulator
E: LysR family transcriptional regulator
F: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,73612
Polymers138,6016
Non-polymers1,1356
Water11,728651
1
A: LysR family transcriptional regulator
D: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5794
Polymers46,2002
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-6 kcal/mol
Surface area18530 Å2
MethodPISA
2
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5794
Polymers46,2002
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-5 kcal/mol
Surface area18580 Å2
MethodPISA
3
E: LysR family transcriptional regulator
F: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5794
Polymers46,2002
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-2 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.788, 111.658, 152.971
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
LysR family transcriptional regulator


Mass: 23100.236 Da / Num. of mol.: 6 / Fragment: UNP residues 88-288
Source method: isolated from a genetically manipulated source
Details: Residues or side chains in disordered region were deleted
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ccpE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2P8TJ56, UniProt: A0A0D1IHL7*PLUS
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4M sodium formate, 10mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9826 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9826 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 118067 / % possible obs: 93.2 % / Redundancy: 4.4 % / Rsym value: 0.152 / Net I/σ(I): 25.02
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.78 / Num. unique obs: 5336 / Rsym value: 0.774 / % possible all: 83.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
HKL-2000data collection
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QBA

4qba


Resolution: 2.5→31.889 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 42.1
RfactorNum. reflection% reflection
Rfree0.2487 961 1.7 %
Rwork0.1981 --
obs0.1989 56606 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→31.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9387 0 78 655 10120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149657
X-RAY DIFFRACTIONf_angle_d1.46613119
X-RAY DIFFRACTIONf_dihedral_angle_d16.1593631
X-RAY DIFFRACTIONf_chiral_restr0.0551492
X-RAY DIFFRACTIONf_plane_restr0.0061706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63180.30581380.27947959X-RAY DIFFRACTION94
2.6318-2.79650.32811410.25188140X-RAY DIFFRACTION96
2.7965-3.01230.28691410.23548218X-RAY DIFFRACTION97
3.0123-3.31520.31951410.21048176X-RAY DIFFRACTION96
3.3152-3.79420.22681380.17687995X-RAY DIFFRACTION94
3.7942-4.77770.16441350.15067812X-RAY DIFFRACTION91
4.7777-31.89160.25911270.18847345X-RAY DIFFRACTION85

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