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- PDB-3tqg: Structure of the 2-methylcitrate synthase (prpC) from Coxiella bu... -

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Basic information

Entry
Database: PDB / ID: 3tqg
TitleStructure of the 2-methylcitrate synthase (prpC) from Coxiella burnetii
Components2-methylcitrate synthase
KeywordsTRANSFERASE / Energy metabolism
Function / homology
Function and homology information


2-methylcitrate synthase activity / propionate catabolic process, 2-methylcitrate cycle / propionate metabolic process, methylcitrate cycle / oxo-acid-lyase activity / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytoplasm
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase ...2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFranklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-methylcitrate synthase
B: 2-methylcitrate synthase


Theoretical massNumber of molelcules
Total (without water)84,7892
Polymers84,7892
Non-polymers00
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-39 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.354, 82.279, 145.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 355
2114B1 - 355
1124A356 - 372
2124B356 - 372

NCS ensembles :
ID
1
2
DetailsChains A and B

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Components

#1: Protein 2-methylcitrate synthase


Mass: 42394.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_0772, prpC / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83DG4, 2-methylcitrate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NaCl, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 32406 / Num. obs: 29397 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.079 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1580 / Rsym value: 0.384 / % possible all: 80.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3HWK

3hwk


Resolution: 2.3→32.94 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.884 / SU B: 18.629 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1524 5.2 %RANDOM
Rwork0.18844 ---
obs0.19188 29348 90.64 %-
all-32379 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.476 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--2.83 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5683 0 0 430 6113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225813
X-RAY DIFFRACTIONr_bond_other_d0.0010.023954
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.967877
X-RAY DIFFRACTIONr_angle_other_deg0.85739625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3485720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41423.712264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48615989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4631538
X-RAY DIFFRACTIONr_chiral_restr0.0620.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021190
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3371.53600
X-RAY DIFFRACTIONr_mcbond_other0.0721.51450
X-RAY DIFFRACTIONr_mcangle_it0.64325773
X-RAY DIFFRACTIONr_scbond_it1.05132213
X-RAY DIFFRACTIONr_scangle_it1.6224.52104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4534medium positional0.410.5
22B261medium positional0.510.5
11A4534medium thermal0.332
22B261medium thermal0.32
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 92 -
Rwork0.25 1748 -
obs--78.4 %
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)
11.3832-0.01240.52210.88150.33411.6431-0.0246-0.19650.15570.13460.0357-0.0267-0.1457-0.0479-0.01110.07610.02820.00750.0858-0.02330.02259.8769-7.931696.2935
21.73340.12750.39491.2042-0.5871.2836-0.040.04230.31130.0488-0.02680.0646-0.1601-0.05350.06680.0395-0.0073-0.00380.057-0.00310.05925.37911.027561.9097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 355
2X-RAY DIFFRACTION1B356 - 372
3X-RAY DIFFRACTION2B11 - 355
4X-RAY DIFFRACTION2A356 - 372

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