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- PDB-3enj: Structure of Pig Heart Citrate Synthase at 1.78 A resolution -

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Basic information

Entry
Database: PDB / ID: 3enj
TitleStructure of Pig Heart Citrate Synthase at 1.78 A resolution
ComponentsCitrate synthase
KeywordsLYASE / TRANSFERASE / disulfide exchange / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for High-Throughput Structural Biology / CHTSB / Methylation / Mitochondrion / Transit peptide / Tricarboxylic acid cycle
Function / homology
Function and homology information


Maturation of TCA enzymes and regulation of TCA cycle / citrate (Si)-synthase / citrate synthase activity / Citric acid cycle (TCA cycle) / : / citrate metabolic process / Mitochondrial protein degradation / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / identical protein binding
Similarity search - Function
Citrate synthase, eukaryotic-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, eukaryotic-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
CYSTEINE / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT PLACEMENT IN SAME UNIT CELL / Resolution: 1.78 Å
AuthorsLarson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A. / Center for High-Throughput Structural Biology (CHTSB)
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of pig heart citrate synthase at 1.78 A resolution.
Authors: Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A.
#1: Journal: CRYST.GROWTH DES. / Year: 2008
Title: Progress in the Development of an Alternative Approach to Macromolecular Crystallization
Authors: Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2304
Polymers48,9771
Non-polymers2533
Water5,386299
1
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4598
Polymers97,9542
Non-polymers5056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9450 Å2
ΔGint-110 kcal/mol
Surface area32420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.340, 76.340, 198.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY THE TWO FOLD AXIS: 1-Y, -X, 1/2-Z

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Components

#1: Protein Citrate synthase


Mass: 48977.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00889, citrate (Si)-synthase
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 295 K / pH: 8.2
Details: 25% PEG 3350 in H2O in the presence of cystamine HCl, aspartame, benzamidine HCl and Tris-HCl buffer, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97839
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97839 Å / Relative weight: 1
ReflectionResolution: 1.72→41.56 Å / Num. obs: 56320 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Redundancy: 6.35 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.3
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 6.07 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
CNS1.2refinement
ADSCQuantumdata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: DIRECT PLACEMENT IN SAME UNIT CELL
Starting model: PDB ENTRY 1CTS

1cts


Resolution: 1.78→41.56 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 8.413 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS FOR ALL NON-WATER MOLECULES HAVE BEEN ADDED IN THE RIDING POSITION AND ADJUSTED TO AVOID STERIC PROBLEMS. OCCUPANCIES FOR HYDROGENS WERE SET TO THE OCCUPANCY OF THE ATOM TO WHICH ...Details: HYDROGENS FOR ALL NON-WATER MOLECULES HAVE BEEN ADDED IN THE RIDING POSITION AND ADJUSTED TO AVOID STERIC PROBLEMS. OCCUPANCIES FOR HYDROGENS WERE SET TO THE OCCUPANCY OF THE ATOM TO WHICH THE HYDROGEN WAS ATTACHED. THE CYSTEAMINE (CYS A 500) COVALENTLY ATTACHED BY A DISULFIDE BOND TO CYSTEINE 184 WAS MODELED AS A CYSTEINE WITH ATOMS C AND O MISSING (SEE REMARK 610). COMMENT ON REMARK 500 BAD TORSION ANGLES. SIDE CHAIN DENSITY IS WEAK AND SIDE CHAIN MAY BE DISORDERED FOR ASP A 295. DENSITY FOR THE LOOP CONTAINING LYS A 366 IS NOT HIGHLY RESOLVED. ARG A 421 IS DISORDERED. ALL OTHERS IN THIS LIST ARE IN WELL-DEFINED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2627 5.1 %RANDOM
Rwork0.179 ---
obs0.181 49141 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.87 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å20 Å2
2--2.21 Å20 Å2
3----4.43 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 0 6 305 7411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223639
X-RAY DIFFRACTIONr_bond_other_d0.0010.023565
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9634957
X-RAY DIFFRACTIONr_angle_other_deg0.7813.0018116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56723.889162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65315634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2611522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
X-RAY DIFFRACTIONr_nbd_refined0.0320.3803
X-RAY DIFFRACTIONr_nbd_other0.080.33518
X-RAY DIFFRACTIONr_nbtor_refined0.0060.51767
X-RAY DIFFRACTIONr_nbtor_other00.52038
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.5325
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0690.5176
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.3115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.534
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1530.514
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.91632224
X-RAY DIFFRACTIONr_mcbond_other0.4583906
X-RAY DIFFRACTIONr_mcangle_it4.61983598
X-RAY DIFFRACTIONr_scbond_it5.35761415
X-RAY DIFFRACTIONr_scangle_it7.705101349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 172 -
Rwork0.386 3128 -
obs--79.67 %
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)
10.6673-0.0139-0.82650.6674-0.92892.60190.132-0.0320.33660.23630.12240.1117-1.0439-0.4966-0.25450.31880.29190.1075-0.02420.06120.069652.59334.95252.981
20.19670.0298-0.05540.6852-0.4583.21480.10960.08880.0333-0.02190.0099-0.0614-0.5670.0558-0.11940.00810.02980.0293-0.08090.00740.024668.97825.04135.044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 54
2X-RAY DIFFRACTION1A411 - 437
3X-RAY DIFFRACTION2A55 - 410
4X-RAY DIFFRACTION2A500

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