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- PDB-5uqu: Crystal structure of mutant 2-methylcitrate synthase (mcsAG352A) ... -

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Basic information

Entry
Database: PDB / ID: 5uqu
TitleCrystal structure of mutant 2-methylcitrate synthase (mcsAG352A) from Aspergillus fumigatus
Components2-methylcitrate synthase, mitochondrial
KeywordsTRANSFERASE / aspergillus fumigatus / 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) / propionate catabolic process / : / tricarboxylic acid cycle / carbohydrate metabolic 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 / 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: 1.7 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

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)98,3307
Polymers97,1432
Non-polymers1,1875
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-109 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.764, 94.151, 123.492
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: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 30 - 464 / Label seq-ID: 6 - 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 1


Mass: 48571.453 Da / Num. of mol.: 2 / Mutation: G352A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: mcsA, cit1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q50I20, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#4: Chemical ChemComp-COA / COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate, 0.1M Tris pH 8.5, 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: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50.01 Å / Num. obs: 81628 / % possible obs: 94.13 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.029 / Rrim(I) all: 0.081 / Rsym value: 0.062 / Net I/σ(I): 35.19
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 3.28 / Num. unique obs: 4534 / CC1/2: 0.857 / Rpim(I) all: 0.278 / Rrim(I) all: 0.785 / Rsym value: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.1 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19213 4122 4.8 %RANDOM
Rwork0.15847 ---
obs0.16003 81628 94.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.724 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å2-0 Å2
2---0.68 Å20 Å2
3---0.84 Å2
Refinement stepCycle: 1 / Resolution: 1.7→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 0 72 749 7617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197057
X-RAY DIFFRACTIONr_bond_other_d00.026611
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.989591
X-RAY DIFFRACTIONr_angle_other_deg3.622315359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40424.153301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.871538
X-RAY DIFFRACTIONr_chiral_restr0.1060.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217808
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021395
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_it1.0651.6083505
X-RAY DIFFRACTIONr_mcbond_other1.0641.6073504
X-RAY DIFFRACTIONr_mcangle_it1.6892.4074381
X-RAY DIFFRACTIONr_mcangle_other1.6892.4084382
X-RAY DIFFRACTIONr_scbond_it1.71.8513552
X-RAY DIFFRACTIONr_scbond_other1.6991.853550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.722.6815207
X-RAY DIFFRACTIONr_long_range_B_refined5.11820.5968257
X-RAY DIFFRACTIONr_long_range_B_other5.11620.5938257
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27522 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 338 -
Rwork0.208 6305 -
obs--99.42 %
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)
11.1388-0.7497-0.57163.93621.57381.0671-0.12140.16030.148-0.33590.2387-0.091-0.17740.101-0.11730.112-0.04660.01030.11960.05080.0534-3.545-11.82411.725
20.57250.22270.11280.6478-0.02950.4254-0.0370.08370.04370.00280.07320.12-0.00520.0026-0.03610.03250.00510.01470.07640.0250.0326-15.817-28.7217.607
31.9228-0.7314-1.08580.5420.48520.75910.1040.05720.0784-0.0354-0.1110.0331-0.0945-0.06790.00710.05840.01670.00230.1009-0.00640.0315-41.675-18.07814.392
40.55250.00540.30310.02820.02440.2472-0.00620.09530.10180.02220.00450.0231-0.04130.01830.00160.10950.0070.05310.10750.05460.1339-21.154-17.36921.531
51.3888-0.0695-0.78030.74290.52012.5014-0.04030.04570.38890.0298-0.06280.2664-0.2082-0.23720.1030.15410.0610.03950.0486-0.01870.2804-20.3780.97637.012
60.49090.36340.0750.80480.17950.40350.0928-0.08530.09440.3127-0.09080.1735-0.003-0.037-0.00190.18770.00130.09350.0705-0.01160.0524-11.538-17.47246.885
70.64930.41050.09840.92530.15960.35620.0281-0.05460.08180.2664-0.00260.0366-0.09350.074-0.02550.16020.00070.02040.07180.00020.02013.36-12.05138.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 71
2X-RAY DIFFRACTION2A72 - 310
3X-RAY DIFFRACTION3A311 - 398
4X-RAY DIFFRACTION4A399 - 465
5X-RAY DIFFRACTION5B30 - 75
6X-RAY DIFFRACTION6B76 - 326
7X-RAY DIFFRACTION7B327 - 465

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