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- PDB-6bon: Crystal structure of 2-methylcitrate synthase from Aspergillus fu... -

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Basic information

Entry
Database: PDB / ID: 6bon
TitleCrystal structure of 2-methylcitrate synthase from Aspergillus fumigatus with oxaloacetate and coenzyme-A.
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 (Si)-synthase activity / tricarboxylic acid cycle / 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 / 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
COENZYME A / OXALOACETATE ION / 2-methylcitrate synthase, mitochondrial
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: 2-methylcitrate synthase, mitochondrial
B: 2-methylcitrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2766
Polymers97,1152
Non-polymers1,1614
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-63 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.869, 93.235, 124.867
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
11A
21B

NCS domain segments:

Component-ID: 0 / 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: 0 / Auth seq-ID: 31 - 464 / Label seq-ID: 7 - 440

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

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Components

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


Mass: 48557.426 Da / Num. of mol.: 2
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-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 28% PEGMME2000 1.0 mM oxaloacetate 1.0 mM coenzyme-A 1.0 mM Guanosine monophosphate

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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: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 32572 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.052 / Rrim(I) all: 0.119 / Rsym value: 0.077 / Net I/σ(I): 14.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 1649 / Rpim(I) all: 0.308 / Rrim(I) all: 0.678 / Rsym value: 0.524 / % possible all: 99.1

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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
Starting model: 5UQO

5uqo


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.748 / ESU R Free: 0.295 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25564 1635 5 %RANDOM
Rwork0.20384 ---
obs0.20644 30916 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.116 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--2.27 Å2-0 Å2
3----1.54 Å2
Refinement stepCycle: 1 / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6744 0 75 145 6964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196982
X-RAY DIFFRACTIONr_bond_other_d00.026529
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9819483
X-RAY DIFFRACTIONr_angle_other_deg3.641315156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0175866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68324.094298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.113151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9841538
X-RAY DIFFRACTIONr_chiral_restr0.0860.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217743
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021384
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_it1.7862.7083470
X-RAY DIFFRACTIONr_mcbond_other1.7842.7083469
X-RAY DIFFRACTIONr_mcangle_it2.9714.0564334
X-RAY DIFFRACTIONr_mcangle_other2.9714.0574335
X-RAY DIFFRACTIONr_scbond_it1.6962.9123512
X-RAY DIFFRACTIONr_scbond_other1.6952.9093510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8484.2815149
X-RAY DIFFRACTIONr_long_range_B_refined4.81532.1017976
X-RAY DIFFRACTIONr_long_range_B_other4.81532.1137977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27276 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 95 -
Rwork0.261 2078 -
obs--87.13 %
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)
10.2483-0.0641-0.1721.5650.67680.5699-0.07410.08720.0206-0.05240.05920.0319-0.04280.04140.01480.0889-0.0336-0.02650.07010.02390.1439-7.415-9.34413.408
20.41760.03970.10980.1258-0.0560.2771-0.02270.03490.0227-0.00640.03930.05530.02530.0417-0.01650.0908-0.0050.00460.0295-0.00020.1745-15.359-30.31618.102
31.0396-0.6861-0.86270.70450.75360.86430.03270.10950.0682-0.0252-0.04440.0054-0.0519-0.07890.01170.0841-0.0022-0.00520.0592-0.00850.1391-40.99-17.34614.312
40.4560.0442-0.13370.04650.03030.1138-0.02740.0432-0.04450.01040.0216-0.016-0.02550.00040.00580.11250.00870.00130.0150.01440.1946-19.934-18.66221.182
50.06240.09560.23210.26230.151.6386-0.0215-0.01920.0876-0.0178-0.05360.1516-0.1513-0.02170.07510.07860.01130.02570.0122-0.03050.2587-17.4641.20436.566
60.250.2526-0.00410.33320.06430.13050.071-0.03570.01760.1247-0.07040.06970.03640.0002-0.00060.1225-0.02760.05060.0378-0.02470.1584-11.748-18.28247.95
70.33950.09670.1640.29440.09310.1537-0.0350.01460.00640.07090.01970.0165-0.00120.02770.01530.11910.00260.00910.00640.00490.16163.044-11.8839.702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 90
2X-RAY DIFFRACTION2A91 - 309
3X-RAY DIFFRACTION3A310 - 402
4X-RAY DIFFRACTION4A403 - 464
5X-RAY DIFFRACTION5B31 - 91
6X-RAY DIFFRACTION6B92 - 327
7X-RAY DIFFRACTION7B328 - 464

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