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

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Basic information

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


citrate (Si)-synthase / citrate (Si)-synthase activity / citrate metabolic process / Citric acid cycle (TCA cycle) / Mitochondrial protein import / Mitochondrial protein degradation / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / mitochondrion ...citrate (Si)-synthase / citrate (Si)-synthase activity / citrate metabolic process / Citric acid cycle (TCA cycle) / Mitochondrial protein import / Mitochondrial protein degradation / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / 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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
D: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5454
Polymers103,4742
Non-polymers712
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-82 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.177, 74.676, 60.652
Angle α, β, γ (deg.)62.78, 93.85, 80.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 30 - 462 / Label seq-ID: 26 - 458

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

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Components

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


Mass: 51736.848 Da / Num. of mol.: 2 / Fragment: residues 28-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CS / Production host: Escherichia coli (E. coli) / References: UniProt: O75390, citrate (Si)-synthase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Acetate pH 7.1, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 35831 / % possible obs: 96.15 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.083 / Rrim(I) all: 0.123 / Rsym value: 0.078 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 1924 / CC1/2: 0.776 / Rpim(I) all: 0.372 / Rrim(I) all: 0.548 / Rsym value: 0.375 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.493 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.229 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21454 1894 5 %RANDOM
Rwork0.17022 ---
obs0.17245 35831 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.323 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20.1 Å20.92 Å2
2---1.16 Å2-0.03 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6852 0 2 400 7254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197026
X-RAY DIFFRACTIONr_bond_other_d0.0060.026506
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9599537
X-RAY DIFFRACTIONr_angle_other_deg1.039315106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7985869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6223.961308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.286151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9261538
X-RAY DIFFRACTIONr_chiral_restr0.0970.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217782
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021424
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_it1.2082.1113476
X-RAY DIFFRACTIONr_mcbond_other1.2052.113475
X-RAY DIFFRACTIONr_mcangle_it2.0693.1614342
X-RAY DIFFRACTIONr_mcangle_other2.073.1624343
X-RAY DIFFRACTIONr_scbond_it1.5072.3043550
X-RAY DIFFRACTIONr_scbond_other1.5062.3053551
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5583.3625195
X-RAY DIFFRACTIONr_long_range_B_refined3.93924.6098102
X-RAY DIFFRACTIONr_long_range_B_other3.89724.4868050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28264 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2D
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 129 -
Rwork0.228 2556 -
obs--93.42 %
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)
10.4398-0.0028-0.01340.49020.05820.401-0.0136-0.00150.0511-0.06950.0098-0.0654-0.03770.03330.00380.0127-0.00370.00570.0028-0.00070.02073.6519-3.55931.0669
20.2168-0.08330.00740.6543-0.25520.4283-0.0053-0.01490.083-0.00250.02660.001-0.0304-0.0514-0.02130.00780.0013-0.00310.01-0.00110.0357-10.49626.2675.7098
30.4654-0.0190.04560.47490.1080.6579-0.0031-0.0042-0.0336-0.01330.00730.07730.0575-0.0708-0.00420.0077-0.00860.00050.0099-0.00090.0282-16.54-26.98548.5918
40.1616-0.0992-0.17620.73840.0140.2243-0.0414-0.0624-0.00870.05810.0347-0.02650.02230.07190.00660.03650.0161-0.00590.0301-0.00210.0212-0.2441-32.988615.7816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 323
2X-RAY DIFFRACTION2A324 - 463
3X-RAY DIFFRACTION3D30 - 249
4X-RAY DIFFRACTION4D250 - 464

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