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- PDB-1xr4: X-ray crystal structure of putative citrate lyase alpha chain/cit... -

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Basic information

Entry
Database: PDB / ID: 1xr4
TitleX-ray crystal structure of putative citrate lyase alpha chain/citrate-ACP transferase [Salmonella typhimurium]
Componentsputative citrate lyase alpha chain/citrate-ACP transferase
KeywordsHYDROLASE/TRANSFERASE / The Midwest Center for Structural Genomics / MCSG / structural genomics / protein structure initiative / PSI / citrate lyase / HYDROLASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


citrate CoA-transferase / citrate CoA-transferase activity / ATP-independent citrate lyase complex / citrate (pro-3S)-lyase / citrate (pro-3S)-lyase activity / citrate metabolic process / acetyl-CoA metabolic process / cytoplasm
Similarity search - Function
Citrate lyase, alpha subunit / Citrate lyase, alpha subunit (CitF) / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / NagB/RpiA transferase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Citrate lyase alpha chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å
AuthorsOsipiuk, J. / Quartey, P. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative citrate lyase alpha chain/citrate-ACP transferase from Salmonella typhimurium.
Authors: Osipiuk, J. / Quartey, P. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative citrate lyase alpha chain/citrate-ACP transferase
B: putative citrate lyase alpha chain/citrate-ACP transferase


Theoretical massNumber of molelcules
Total (without water)110,8922
Polymers110,8922
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-22 kcal/mol
Surface area36320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.374, 116.701, 189.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein putative citrate lyase alpha chain/citrate-ACP transferase


Mass: 55445.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: CitF / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZRY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris_HCl, PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979565 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 27, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979565 Å / Relative weight: 1
ReflectionResolution: 2.37→40 Å / Num. all: 53458 / Num. obs: 49002 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 13.34
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 5 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.85 / Num. unique all: 2256 / % possible all: 51.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.37→40 Å / Cor.coef. Fo:Fc: 0.946 / SU B: 11.417 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The test data set was not used in last round of refinement. The deposited pdb file is from the last round of refinement. R-factor-obs and R- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The test data set was not used in last round of refinement. The deposited pdb file is from the last round of refinement. R-factor-obs and R-factor-all correspond to deposited file. R-factor-work and R-factor-free are taken from second to last round of refinement which used test data set.
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 1990 -RANDOM
Rwork0.193 ---
all0.1908 48980 --
obs0.19084 46990 91.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.982 Å2
Baniso -1Baniso -2Baniso -3
1-4.72 Å20 Å20 Å2
2---1.04 Å20 Å2
3----3.68 Å2
Refinement stepCycle: LAST / Resolution: 2.37→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7654 0 0 287 7941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227772
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.95810530
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31551010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50824.327342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.232151326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9341558
X-RAY DIFFRACTIONr_chiral_restr0.0910.21222
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025854
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.23457
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25332
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2351
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8461.55120
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2728034
X-RAY DIFFRACTIONr_scbond_it2.17832908
X-RAY DIFFRACTIONr_scangle_it3.4044.52496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.373→2.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 69 -
Rwork0.282 2008 -
obs-1939 51.74 %
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)
10.1515-0.00760.19560.7248-0.57231.18610.02810.01190.0167-0.0568-0.022-0.01660.079-0.0545-0.0061-0.03640.02170.0048-0.0573-0.0029-0.045532.484258.48538.2098
20.2653-0.15930.08230.3056-0.21221.43170.0327-0.0499-0.01950.0864-0.0368-0.057-0.0958-0.11090.0041-0.0295-0.0196-0.0292-0.0345-0.0037-0.073833.918254.510281.3463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA39 - 50542 - 508
2X-RAY DIFFRACTION1BB1 - 384 - 41
3X-RAY DIFFRACTION2AA1 - 384 - 41
4X-RAY DIFFRACTION2BB39 - 50542 - 508

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