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- PDB-6bol: Crystal structure of mutant 2-methylcitrate synthase mcsAG419A fr... -

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Basic information

Entry
Database: PDB / ID: 6bol
TitleCrystal structure of mutant 2-methylcitrate synthase mcsAG419A 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 / propionate catabolic process, 2-methylcitrate cycle / citrate synthase (unknown stereospecificity) / citrate synthase activity / : / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / identical protein binding
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 / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily ...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 / PHOSPHATE ION / 2-methylcitrate synthase, mitochondrial
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 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 13, 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
B: 2-methylcitrate synthase, mitochondrial
A: 2-methylcitrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7258
Polymers97,1432
Non-polymers5826
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-99 kcal/mol
Surface area30500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.641, 103.595, 135.149
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: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 32 - 463 / Label seq-ID: 8 - 439

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 2


Mass: 48571.453 Da / Num. of mol.: 2 / Mutation: G419A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: mcsA, AFUB_094700 / Production host: Escherichia coli (E. coli)
References: UniProt: B0YD89, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Tris pH 7.5 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 47254 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.072 / Rrim(I) all: 0.186 / Rsym value: 0.249 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 2298 / Rpim(I) all: 0.308 / Rrim(I) all: 0.738 / Rsym value: 0.872 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing
RefinementResolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26212 2119 4.8 %RANDOM
Rwork0.20417 ---
obs0.20694 41927 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6717 0 34 224 6975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196909
X-RAY DIFFRACTIONr_bond_other_d00.026447
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9739387
X-RAY DIFFRACTIONr_angle_other_deg3.745314961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85324.189296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1131536
X-RAY DIFFRACTIONr_chiral_restr0.1010.21041
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217687
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021365
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_it1.0582.053466
X-RAY DIFFRACTIONr_mcbond_other1.0582.053465
X-RAY DIFFRACTIONr_mcangle_it1.8233.0714329
X-RAY DIFFRACTIONr_mcangle_other1.8233.0714330
X-RAY DIFFRACTIONr_scbond_it1.262.2643443
X-RAY DIFFRACTIONr_scbond_other1.2232.2393429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0423.295040
X-RAY DIFFRACTIONr_long_range_B_refined3.85224.3377810
X-RAY DIFFRACTIONr_long_range_B_other3.85224.3517811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27148 / 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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 124 -
Rwork0.225 2364 -
obs--74.07 %
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)
10.55380.25010.26870.63570.16060.8441-0.00080.06580.008-0.0239-0.02660.0056-0.08850.03830.02740.0287-0.0115-0.00060.0234-0.00130.0574-10.01510.356-36.506
21.7513-1.1815-1.20321.55510.84632.1816-0.1141-0.0188-0.0172-0.01310.11010.0917-0.08870.02470.00410.0638-0.0079-0.01350.0163-0.00770.1058-27.41530.341-29.766
30.5605-0.0955-0.87980.7340.22321.53780.0376-0.0004-0.00530.058-0.01660.0007-0.21870.094-0.0210.2015-0.10080.00550.09440.01160.1074-3.56714.368-26.025
40.53110.05720.0990.4649-0.07381.0423-0.016-0.04360.01440.0636-0.00720.0102-0.03710.03240.02320.0391-0.01210.0040.0104-0.00050.0513-5.966.551-5.942
53.06550.1784-2.05191.45490.09011.8246-0.22260.008-0.2862-0.00930.2876-0.23680.030.1908-0.0650.1167-0.06330.06310.1324-0.09620.234218.02-7.172-9.437
60.95430.0928-0.00930.18270.29090.5566-0.05870.00180.0172-0.0290.0370.0028-0.08970.03530.02160.0893-0.0056-0.01420.02930.00210.0657-2.53813.509-16.599
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 311
2X-RAY DIFFRACTION2A312 - 423
3X-RAY DIFFRACTION3A424 - 464
4X-RAY DIFFRACTION4B31 - 310
5X-RAY DIFFRACTION5B311 - 423
6X-RAY DIFFRACTION6B424 - 464

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