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- PDB-5uzq: Crystal structure of citrate synthase from homo sapiens -

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Basic information

Entry
Database: PDB / ID: 5uzq
TitleCrystal structure of citrate synthase from homo sapiens
ComponentsCitrate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


citrate (Si)-synthase / Citric acid cycle (TCA cycle) / : / citrate metabolic process / Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / carbohydrate metabolic process / mitochondrial matrix ...citrate (Si)-synthase / Citric acid cycle (TCA cycle) / : / citrate metabolic process / Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / identical protein binding / nucleus
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 / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)51,8891
Polymers51,8891
Non-polymers00
Water2,864159
1
A: Citrate synthase

A: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)103,7782
Polymers103,7782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8700 Å2
ΔGint-64 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.760, 76.760, 198.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-599-

HOH

21A-610-

HOH

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Components

#1: Protein Citrate synthase


Mass: 51889.086 Da / Num. of mol.: 1 / Fragment: residues 15-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CS / Production host: Escherichia coli (E. coli) / References: UniProt: B4DJV2, UniProt: O75390*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1 M Succinic Acid pH 7.0, 12% 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: Aug 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50.01 Å / Num. obs: 29021 / % possible obs: 93.01 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Rsym value: 0.068 / Net I/σ(I): 25.87
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.29 / Num. unique obs: 1500 / CC1/2: 0.968 / Rpim(I) all: 0.148 / Rrim(I) all: 0.483 / Rsym value: 0.323 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.184 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23232 1551 5.1 %RANDOM
Rwork0.19596 ---
obs0.19789 29021 93.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.369 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å2-0 Å20 Å2
2--2.48 Å20 Å2
3----4.95 Å2
Refinement stepCycle: 1 / Resolution: 2.16→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 0 159 3585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193511
X-RAY DIFFRACTIONr_bond_other_d00.023245
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9624764
X-RAY DIFFRACTIONr_angle_other_deg3.72637533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89423.961154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6415590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9941519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213884
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02711
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_it0.9842.7541735
X-RAY DIFFRACTIONr_mcbond_other0.9822.7521734
X-RAY DIFFRACTIONr_mcangle_it1.6664.1262167
X-RAY DIFFRACTIONr_mcangle_other1.6664.1282168
X-RAY DIFFRACTIONr_scbond_it1.0872.8871775
X-RAY DIFFRACTIONr_scbond_other1.0872.8871775
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8354.2692598
X-RAY DIFFRACTIONr_long_range_B_refined4.31751.34414448
X-RAY DIFFRACTIONr_long_range_B_other4.26151.13714368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 101 -
Rwork0.274 1907 -
obs--84.19 %
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)
11.0801-0.00820.33133.5619-0.28335.15280.0313-0.07470.02960.13660.0610.44360.7096-2.0139-0.09220.1276-0.33580.00950.93640.02590.0762-39.351-19.4793.145
20.4457-0.02970.35230.7790.22373.598-0.00970.02140.1047-0.06030.0264-0.0027-0.4473-0.8226-0.01680.12180.04680.02460.28530.00760.14-25.246-3.896-5.981
33.4060.83845.12041.19081.966211.71510.00830.343-0.01330.2310.0396-0.04440.36520.414-0.04790.07-0.04370.00690.2269-0.00490.1427-19.24-16.141-36.971
40.94850.89160.11983.20270.17594.12960.05220.128-0.0062-0.0039-0.045-0.04250.3022-0.7104-0.00720.0955-0.1452-0.04680.40580.01420.0671-29.61-17.333-31.084
50.40250.19880.07930.28690.26653.52160.01640.0563-0.0294-0.00880.0269-0.00660.3513-0.8885-0.04320.1231-0.15670.00150.3080.01070.142-24.833-17.392-7.804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 73
2X-RAY DIFFRACTION2A74 - 305
3X-RAY DIFFRACTION3A306 - 329
4X-RAY DIFFRACTION4A330 - 397
5X-RAY DIFFRACTION5A398 - 463

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