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- PDB-5uqo: Crystal structure of 2-methylcitrate synthase from Aspergillus fu... -

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Basic information

Entry
Database: PDB / ID: 5uqo
TitleCrystal structure of 2-methylcitrate synthase from Aspergillus fumigatus
Components2-methylcitrate synthase, mitochondrial
KeywordsTRANSFERASE / mcsA / 2-methylcitrate synthase / citrate synthase
Function / homology
Function and homology information


2-methylcitrate synthase / 2-methylcitrate synthase activity / citrate synthase (unknown stereospecificity) / citrate synthase activity / propionate catabolic process / mitochondrial matrix
Similarity search - Function
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-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain ...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-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-methylcitrate synthase, mitochondrial
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1Jun 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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

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Assembly

Deposited unit
B: 2-methylcitrate synthase, mitochondrial
A: 2-methylcitrate synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)102,0582
Polymers102,0582
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-65 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.548, 116.333, 153.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 31 - 464 / Label seq-ID: 28 - 461

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein 2-methylcitrate synthase, mitochondrial / Methylcitrate synthase / (2S / 3S)-2-methylcitrate synthase / Citrate synthase 1


Mass: 51029.078 Da / Num. of mol.: 2 / Fragment: UNP residues 29-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: mcsA, cit1 / Plasmid: pJExpress411 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: Q50I20, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaTartrate dibasic dihydrate, 20% PEG3350 pH 7.3

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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: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50.01 Å / Num. obs: 34715 / % possible obs: 95.05 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Rrim(I) all: 0.104 / Rsym value: 0.066 / Net I/σ(I): 21.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 1814 / CC1/2: 0.806 / Rpim(I) all: 0.318 / Rrim(I) all: 0.724 / Rsym value: 0.59 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 23.847 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.48 / ESU R Free: 0.268 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1830 5 %RANDOM
Rwork0.19106 ---
obs0.19314 34715 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.911 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å2-0 Å20 Å2
2--3.01 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6759 0 0 100 6859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196922
X-RAY DIFFRACTIONr_bond_other_d0.0060.026541
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9719390
X-RAY DIFFRACTIONr_angle_other_deg1.024315190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.524.108297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.591151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1611538
X-RAY DIFFRACTIONr_chiral_restr0.0880.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217674
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021372
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_it1.9743.8683470
X-RAY DIFFRACTIONr_mcbond_other1.9733.8683469
X-RAY DIFFRACTIONr_mcangle_it3.3525.7974334
X-RAY DIFFRACTIONr_mcangle_other3.3525.7974335
X-RAY DIFFRACTIONr_scbond_it2.2224.1893452
X-RAY DIFFRACTIONr_scbond_other2.2214.193453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8356.1315057
X-RAY DIFFRACTIONr_long_range_B_refined5.6444.997761
X-RAY DIFFRACTIONr_long_range_B_other5.63744.9897759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27156 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 132 -
Rwork0.303 2504 -
obs--94.79 %
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)
10.72470.0763-0.04150.7453-0.10641.65690.0695-0.1944-0.13590.0277-0.0539-0.125-0.01920.3712-0.01560.0086-0.0391-0.01550.34770.02960.0431-6.76531.55932.5109
21.19480.1357-1.11951.0654-0.7863.98-0.01920.1147-0.0457-0.07580.1351-0.02210.3446-0.4271-0.11590.1096-0.1101-0.04620.31380.09610.042-26.6082-13.364515.5637
30.34820.5561-0.03161.0363-0.09991.5813-0.0362-0.0263-0.1735-0.0639-0.0129-0.19660.16750.1590.04920.053-0.0030.01970.32180.00340.1365-14.1432-0.6522-8.3004
40.5459-0.1841-0.21231.1992-0.11111.34340.06140.0248-0.0602-0.05920.05590.1449-0.1321-0.2069-0.11730.0345-0.00090.00460.2759-0.00560.0357-28.621113.1939-17.0023
52.231.0811-1.01625.54331.64453.5333-0.0531-0.0443-0.20.08760.06990.132-0.37610.6498-0.01670.197-0.13460.02620.3732-0.0790.0607-2.485718.8928-35.945
60.60770.0287-0.41680.1556-0.48031.87540.06180.1349-0.0947-0.00750.05380.0378-0.1384-0.0073-0.11560.1314-0.08430.01850.306-0.06840.041-16.261313.2943-27.343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 309
2X-RAY DIFFRACTION2A310 - 423
3X-RAY DIFFRACTION3A424 - 464
4X-RAY DIFFRACTION4B31 - 309
5X-RAY DIFFRACTION5B310 - 355
6X-RAY DIFFRACTION6B356 - 464

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