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- PDB-7xbe: co-crystal structure of CcpE-RD with citrate -

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Basic information

Entry
Database: PDB / ID: 7xbe
Titleco-crystal structure of CcpE-RD with citrate
ComponentsLysR family transcriptional regulator
KeywordsTRANSCRIPTION / LysR family transcriptional regulator
Function / homologyCITRATE ANION / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLan, L.F. / Chen, F.F. / Gan, J.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670136 China
National Natural Science Foundation of China (NSFC)31700124 China
National Natural Science Foundation of China (NSFC)81861138047 China
CitationJournal: To Be Published
Title: co-crystal structure of CcpE-RD with citrate
Authors: Lan, L.F. / Chen, F.F. / Gan, J.H.
History
DepositionMar 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5154
Polymers33,2801
Non-polymers2353
Water1,45981
1
A: LysR family transcriptional regulator
hetero molecules

A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0318
Polymers66,5602
Non-polymers4706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3990 Å2
ΔGint-51 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.935, 38.799, 54.504
Angle α, β, γ (deg.)90.000, 118.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LysR family transcriptional regulator


Mass: 33280.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: M013TW_0659 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U4ASJ0
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.43 Å3/Da / Density % sol: 13.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate, pH 4.6, 25 % (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 22631 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.064 / Rrim(I) all: 0.115 / Χ2: 1.073 / Net I/σ(I): 7.8 / Num. measured all: 73578
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.683.10.49810770.8120.3310.61.03897.1
1.68-1.713.20.44411470.8380.2880.5311.07198.3
1.71-1.743.30.42110920.8580.2680.5011.10598.1
1.74-1.783.30.35611300.8770.2310.4261.07698.3
1.78-1.823.30.30711500.9110.20.3681.08398.3
1.82-1.863.10.25511120.9210.1730.3091.09698.5
1.86-1.93.20.23911070.9610.1580.2871.05398.6
1.9-1.963.40.20411340.9560.1340.2451.22398.4
1.96-2.013.40.17911170.9590.1160.2141.12398.4
2.01-2.083.40.16711310.9570.1080.1991.06498.7
2.08-2.153.30.1511450.960.10.1811.11198.5
2.15-2.243.10.13711160.9640.0920.1651.10698.7
2.24-2.343.20.12511320.9690.0840.1511.02298.7
2.34-2.463.40.1211320.9770.0790.1441.02498.2
2.46-2.623.40.11211440.9730.0730.1351.05298.8
2.62-2.823.20.10111300.9720.0680.1220.96298.9
2.82-3.113.20.09811370.9810.0650.1181.06298.3
3.11-3.553.30.08911540.980.0590.1071.09299.1
3.55-4.4830.08311600.9830.0570.1011.00398.1
4.48-503.10.0811840.9860.0530.0961.06897.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZZO

5zzo


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.829 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 1119 5 %RANDOM
Rwork0.1886 ---
obs0.1904 21396 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.4 Å2 / Biso mean: 33.795 Å2 / Biso min: 18.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.1 Å2-0 Å2-0.65 Å2
2--1.39 Å2-0 Å2
3---1.53 Å2
Refinement stepCycle: final / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 15 81 1687
Biso mean--31.34 38.13 -
Num. residues----197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191662
X-RAY DIFFRACTIONr_bond_other_d0.0020.021501
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9572264
X-RAY DIFFRACTIONr_angle_other_deg0.86633510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.615204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41525.90483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76515292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.038155
X-RAY DIFFRACTIONr_chiral_restr0.1930.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02312
X-RAY DIFFRACTIONr_rigid_bond_restr0.77333163
X-RAY DIFFRACTIONr_sphericity_free24.364553
X-RAY DIFFRACTIONr_sphericity_bonded4.00253157
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 89 -
Rwork0.253 1534 -
all-1623 -
obs--97.65 %
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)
14.04770.07570.13330.43240.06760.0674-0.0194-0.4676-0.2882-0.0767-0.00750.0083-0.0301-0.04360.02690.08260.00790.01450.09190.01860.053751.30216.20114.935
22.0607-0.45830.29540.4224-0.23590.6983-0.0073-0.00920.1592-0.0383-0.0134-0.01960.00350.01830.02070.1146-0.00180.03770.0175-0.01630.039634.36626.341-2.118
34.7597-0.3114-2.65120.437-0.40692.2915-0.2797-1.3404-0.18670.05250.29230.08750.09060.4198-0.01260.06160.08840.02210.54850.07060.030850.66216.622.987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 159
2X-RAY DIFFRACTION2A160 - 256
3X-RAY DIFFRACTION3A257 - 284

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