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- PDB-7dmw: Crystal structure of CcpC regulatory domain in complex with citra... -

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Basic information

Entry
Database: PDB / ID: 7dmw
TitleCrystal structure of CcpC regulatory domain in complex with citrate from Bacillus amyloliquefaciens
ComponentsCcpC
KeywordsTRANSCRIPTION / CcpC / Complex / Bacillus amyloliquefaciens / Transcriptional regulator / citrate
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
CITRATE ANION / LysR family transcriptional regulator
Similarity search - Component
Biological speciesBacillus velezensis FZB42 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsChen, J. / Wang, L. / Shang, F. / Liu, W. / Chen, Y. / Lan, J. / Bu, T. / Bai, X. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31200556 China
National Natural Science Foundation of China (NSFC)21272031 China
CitationJournal: Sci Rep / Year: 2021
Title: Functional and structural analysis of catabolite control protein C that responds to citrate.
Authors: Liu, W. / Chen, J. / Jin, L. / Liu, Z.Y. / Lu, M. / Jiang, G. / Yang, Q. / Quan, C. / Nam, K.H. / Xu, Y.
History
DepositionDec 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CcpC
B: CcpC
C: CcpC
D: CcpC
E: CcpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,10110
Polymers170,1565
Non-polymers9465
Water2,756153
1
A: CcpC
C: CcpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4404
Polymers68,0622
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-10 kcal/mol
Surface area18370 Å2
MethodPISA
2
B: CcpC
hetero molecules

B: CcpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4404
Polymers68,0622
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3400 Å2
ΔGint-6 kcal/mol
Surface area18100 Å2
MethodPISA
3
D: CcpC
E: CcpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4404
Polymers68,0622
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-10 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.963, 90.898, 105.531
Angle α, β, γ (deg.)90.000, 106.178, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
CcpC


Mass: 34031.148 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus velezensis FZB42 (bacteria) / Strain: FZB42 / Gene: ccpC, RBAM_013910 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A7Z428
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 6000 5% MPD 0.1 M HEPES (pH7.5) / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
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: 2.29→50 Å / Num. obs: 55746 / % possible obs: 96.53 % / Redundancy: 5.3 % / Biso Wilson estimate: 48.74 Å2 / Rsym value: 0.08 / Net I/σ(I): 36.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.64 / Num. unique obs: 2427 / Rsym value: 0.31 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.29→29.71 Å / SU ML: 0.3891 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 32.379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.267 1999 3.59 %
Rwork0.2075 53718 -
obs0.2096 55717 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62 Å2
Refinement stepCycle: LAST / Resolution: 2.29→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7976 0 65 153 8194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088239
X-RAY DIFFRACTIONf_angle_d0.946311174
X-RAY DIFFRACTIONf_chiral_restr0.05381234
X-RAY DIFFRACTIONf_plane_restr0.00541390
X-RAY DIFFRACTIONf_dihedral_angle_d6.21694906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.41221160.34773113X-RAY DIFFRACTION78.58
2.35-2.410.39831390.33873756X-RAY DIFFRACTION95.16
2.41-2.480.381440.31573846X-RAY DIFFRACTION96.92
2.48-2.560.35421420.28463851X-RAY DIFFRACTION97.68
2.56-2.650.31521440.25913865X-RAY DIFFRACTION98.09
2.65-2.760.3241460.24763910X-RAY DIFFRACTION98.47
2.76-2.880.29751460.23073944X-RAY DIFFRACTION98.79
2.88-3.040.30941460.23433907X-RAY DIFFRACTION99.05
3.04-3.230.29151480.23013960X-RAY DIFFRACTION99.25
3.23-3.470.27681460.20523932X-RAY DIFFRACTION99.44
3.47-3.820.24181460.19753926X-RAY DIFFRACTION98.29
3.82-4.380.23761480.17383969X-RAY DIFFRACTION99.56
4.38-5.510.19751470.16013949X-RAY DIFFRACTION99.03
5.51-29.710.25881410.18853790X-RAY DIFFRACTION92.84

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