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- PDB-5uqs: Crystal structure of Citrate synthase from Sus scrofa -

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Basic information

Entry
Database: PDB / ID: 5uqs
TitleCrystal structure of Citrate synthase from Sus scrofa
ComponentsCitrate synthase, mitochondrial
KeywordsTRANSFERASE / porcine citrate synthase
Function / homology
Function and homology information


Maturation of TCA enzymes and regulation of TCA cycle / citrate (Si)-synthase / Citric acid cycle (TCA cycle) / citrate synthase activity / : / 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
Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchlachter, C. / Chruszcz, M.
CitationJournal: Biol.Chem. / Year: 2019
Title: Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase.
Authors: Schlachter, C.R. / Klapper, V. / Radford, T. / Chruszcz, M.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 17, 2020Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / entity_src_nat
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.src_method
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citrate synthase, mitochondrial
C: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4544
Polymers103,3832
Non-polymers712
Water19,0601058
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-76 kcal/mol
Surface area31820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.575, 59.884, 74.761
Angle α, β, γ (deg.)99.60, 98.47, 117.53
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 31 - 462 / Label seq-ID: 31 - 462

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

#1: Protein Citrate synthase, mitochondrial / Citrate (Si)-synthase


Mass: 51691.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00889, citrate (Si)-synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1058 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 NaTartrate pH 7.85, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50.01 Å / Num. obs: 104042 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.046 / Rrim(I) all: 0.068 / Rsym value: 0.061 / Net I/σ(I): 19.95
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 5428 / CC1/2: 0.733 / Rpim(I) all: 0.359 / Rrim(I) all: 0.53 / Rsym value: 0.344 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ENJ

3enj


Resolution: 1.6→34 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17844 5481 5 %RANDOM
Rwork0.15253 ---
obs0.15384 104042 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.04 Å2-0.05 Å2
2---0.1 Å20.12 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.6→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6849 0 2 1058 7909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197070
X-RAY DIFFRACTIONr_bond_other_d00.026578
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9629607
X-RAY DIFFRACTIONr_angle_other_deg3.604315283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4325882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57724.026308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.703151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4211538
X-RAY DIFFRACTIONr_chiral_restr0.1040.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217834
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021420
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_it0.9591.373492
X-RAY DIFFRACTIONr_mcbond_other0.9591.3693491
X-RAY DIFFRACTIONr_mcangle_it1.6312.0494368
X-RAY DIFFRACTIONr_mcangle_other1.6312.054369
X-RAY DIFFRACTIONr_scbond_it1.3471.563578
X-RAY DIFFRACTIONr_scbond_other1.3471.563578
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1972.265234
X-RAY DIFFRACTIONr_long_range_B_refined4.61927.42231673
X-RAY DIFFRACTIONr_long_range_B_other4.25725.94530367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28650 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 391 -
Rwork0.24 7428 -
obs--93.54 %
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)
16.6566.59870.73917.2133-1.26786.1086-0.24150.2544-0.2159-0.4651-0.0557-0.33770.67930.92790.29720.1130.08610.05780.23750.02130.166821.678-0.1293.644
20.3105-0.0345-0.02950.28570.080.57510.01420.05880.0017-0.02040.0006-0.04110.03650.0973-0.01490.01340.00540.00130.0331-0.00050.00625.4980.1144.695
31.0433-0.69940.50381.7739-0.1260.9205-0.02020.01410.0588-0.0524-0.04550.19420.0258-0.10140.06570.0253-0.0014-0.02370.078-0.02420.0557-15.8244.192-12.567
40.1824-0.22520.05510.40210.08130.751-0.03560.02450.02380.00620.0022-0.0006-0.07120.0340.03350.0257-0.0177-0.00280.02-0.00060.0321-1.62711.49615.74
50.1037-0.1511-0.25290.91650.09610.913-0.00360.0395-0.01290.005300.16-0.0915-0.14230.00360.05030.0108-0.01290.02370.00650.0682-18.04417.38221.766
60.1782-0.03170.1180.42410.29161.2470.0027-0.0388-0.00170.1243-0.04340.06120.1937-0.16410.04070.0604-0.03460.01990.039-0.0030.0122-13.142-2.830.283
70.55060.69280.28331.32790.37391.2345-0.0837-0.03690.0091-0.05710.1173-0.04690.03740.1303-0.03370.06110.0269-0.01810.0811-0.0250.01057.1966.30346.705
80.0315-0.03090.09160.47360.15350.8865-0.0145-0.01980.01720.0131-0.0313-0.0209-0.0362-0.02850.04580.02110.0035-0.00530.03820.0050.0373-6.8599.73118.472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 34
2X-RAY DIFFRACTION2A35 - 302
3X-RAY DIFFRACTION3A303 - 420
4X-RAY DIFFRACTION4A421 - 464
5X-RAY DIFFRACTION5C30 - 73
6X-RAY DIFFRACTION6C74 - 307
7X-RAY DIFFRACTION7C308 - 418
8X-RAY DIFFRACTION8C419 - 463

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