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- PDB-5z72: Crystal structure of CcpC regulatory domain in complex with citra... -

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Basic information

Entry
Database: PDB / ID: 5z72
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChen, J. / Wang, L. / Shang, F. / Xu, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaGrant No. 31200556 China
National Natural Science Foundation of China21272031 China
Program for Liaoning Excellent Talents in UniversityLJQ2015030 China
CitationJournal: To Be Published
Title: Mechanistic insights from the crystal structures of a catabolite control protein C on citrate-responsive mechanism
Authors: Chen, J. / Wang, L. / Dong, Y. / Ha, N.C.
History
DepositionJan 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)171,37722
Polymers170,1565
Non-polymers1,22117
Water5,260292
1
A: CcpC
C: CcpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5328
Polymers68,0622
Non-polymers4706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-46 kcal/mol
Surface area18280 Å2
MethodPISA
2
B: CcpC
hetero molecules

B: CcpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,57810
Polymers68,0622
Non-polymers5168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4100 Å2
ΔGint-87 kcal/mol
Surface area17910 Å2
MethodPISA
3
D: CcpC
E: CcpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5559
Polymers68,0622
Non-polymers4937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-48 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.963, 90.898, 105.531
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number5
Space group name H-MC121

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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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 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
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: 2.3→50 Å / Num. obs: 55746 / % possible obs: 96.53 % / Redundancy: 5.3 % / 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
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.712 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 1764 3.59 %
Rwork0.185 --
obs0.1875 49153 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7861 0 77 293 8231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168127
X-RAY DIFFRACTIONf_angle_d1.61611015
X-RAY DIFFRACTIONf_dihedral_angle_d19.0313060
X-RAY DIFFRACTIONf_chiral_restr0.0631218
X-RAY DIFFRACTIONf_plane_restr0.0081365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.37431330.31543565X-RAY DIFFRACTION97
2.4649-2.53740.37191340.28443603X-RAY DIFFRACTION98
2.5374-2.61920.33061340.25933609X-RAY DIFFRACTION98
2.6192-2.71280.2931360.23393658X-RAY DIFFRACTION99
2.7128-2.82130.31721350.22933624X-RAY DIFFRACTION98
2.8213-2.94960.28421370.22153664X-RAY DIFFRACTION99
2.9496-3.10490.34431370.21533692X-RAY DIFFRACTION99
3.1049-3.29930.26761360.19923667X-RAY DIFFRACTION99
3.2993-3.55360.23211380.18573681X-RAY DIFFRACTION99
3.5536-3.91050.23641360.16823676X-RAY DIFFRACTION99
3.9105-4.47470.2341390.14583708X-RAY DIFFRACTION99
4.4747-5.63140.19431380.14563734X-RAY DIFFRACTION99
5.6314-29.7140.25161310.17713508X-RAY DIFFRACTION92

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