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- PDB-5uzp: Crystal structure of citrate synthase mutant A348G from homo sapiens -

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Basic information

Entry
Database: PDB / ID: 5uzp
TitleCrystal structure of citrate synthase mutant A348G from homo sapiens
ComponentsCitrate synthase, mitochondrial
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
OXALOACETATE ION / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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
B: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7084
Polymers103,4462
Non-polymers2622
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-54 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.245, 111.804, 74.162
Angle α, β, γ (deg.)90.00, 99.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 28 - 463 / Label seq-ID: 24 - 459

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

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Components

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


Mass: 51722.820 Da / Num. of mol.: 2 / Fragment: residues 28-466 / Mutation: A348G
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-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Acetate, 0.1 NaCitrate tribasic dihydrate pH 5.6, 15% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40046 / % possible obs: 99.59 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.091 / Rrim(I) all: 0.176 / Rsym value: 0.129 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2413 / CC1/2: 0.649 / Rpim(I) all: 0.618 / Rrim(I) all: 1.194 / Rsym value: 0.768 / % possible all: 99.9

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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: 2.29→45.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.57 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.207 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20549 1974 4.7 %RANDOM
Rwork0.15592 ---
obs0.15824 40046 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.633 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-0 Å2-0.62 Å2
2--2.73 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 2.29→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6839 0 18 576 7433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197056
X-RAY DIFFRACTIONr_bond_other_d0.0060.026478
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9599588
X-RAY DIFFRACTIONr_angle_other_deg1.031315039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09524.019311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.779151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9951538
X-RAY DIFFRACTIONr_chiral_restr0.0970.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217867
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021431
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_it2.2622.6243497
X-RAY DIFFRACTIONr_mcbond_other2.2622.6223496
X-RAY DIFFRACTIONr_mcangle_it3.5743.9264371
X-RAY DIFFRACTIONr_mcangle_other3.5743.9284372
X-RAY DIFFRACTIONr_scbond_it2.9532.9223559
X-RAY DIFFRACTIONr_scbond_other2.9472.9233557
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6794.2375214
X-RAY DIFFRACTIONr_long_range_B_refined6.18730.7128365
X-RAY DIFFRACTIONr_long_range_B_other6.16430.5678255
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28080 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 146 -
Rwork0.213 2811 -
obs--95.26 %

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