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

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Basic information

Entry
Database: PDB / ID: 6boo
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 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
COENZYME A / OXALOACETATE ION / 2-methylcitrate synthase, mitochondrial
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
B: 2-methylcitrate synthase, mitochondrial
A: 2-methylcitrate synthase, mitochondrial
C: 2-methylcitrate synthase, mitochondrial
D: 2-methylcitrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,42011
Polymers194,2304
Non-polymers2,1907
Water3,531196
1
B: 2-methylcitrate synthase, mitochondrial
C: 2-methylcitrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2766
Polymers97,1152
Non-polymers1,1614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-62 kcal/mol
Surface area29220 Å2
MethodPISA
2
A: 2-methylcitrate synthase, mitochondrial
D: 2-methylcitrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1455
Polymers97,1152
Non-polymers1,0303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-65 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.882, 68.785, 123.997
Angle α, β, γ (deg.)90.00, 89.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:

Component-ID: _ / 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 - 465 / Label seq-ID: 7 - 441

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BA
21AB
12BA
22CC
13BA
23DD
14AB
24CC
15AB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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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.: 4
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


Mass: 131.064 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 6.5 28% PEGMME2000 1.0 mM oxaloacetate 1.0 mM coenzyme-A

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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: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 47339 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.056 / Rrim(I) all: 0.103 / Rsym value: 0.068 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 2362 / Rpim(I) all: 0.346 / Rrim(I) all: 0.622 / Rsym value: 0.437 / % possible all: 95.4

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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: 2.6→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23683 2163 4.7 %RANDOM
Rwork0.19913 ---
obs0.20091 43765 94.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.361 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å2-0 Å2-0.55 Å2
2--0.7 Å2-0 Å2
3----2.91 Å2
Refinement stepCycle: 1 / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13518 0 141 196 13855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01914002
X-RAY DIFFRACTIONr_bond_other_d00.0213109
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.98219012
X-RAY DIFFRACTIONr_angle_other_deg3.627330435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31151736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30924.108594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.946152331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7571575
X-RAY DIFFRACTIONr_chiral_restr0.0840.22096
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115517
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022768
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_it1.2393.2326956
X-RAY DIFFRACTIONr_mcbond_other1.2393.2326955
X-RAY DIFFRACTIONr_mcangle_it2.2314.8458688
X-RAY DIFFRACTIONr_mcangle_other2.2314.8468689
X-RAY DIFFRACTIONr_scbond_it1.0023.3387046
X-RAY DIFFRACTIONr_scbond_other1.0023.3387047
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8284.95210325
X-RAY DIFFRACTIONr_long_range_B_refined3.5938.46716273
X-RAY DIFFRACTIONr_long_range_B_other3.5938.46616274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B297240.04
12A297240.04
21B285200.08
22C285200.08
31B285980.08
32D285980.08
41A285200.08
42C285200.08
51A285980.08
52D285980.08
61C292800.04
62D292800.04
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 164 -
Rwork0.297 3218 -
obs--95.46 %
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)
10.8045-0.3442-0.13460.78140.19660.4566-0.0928-0.213-0.15360.13060.05520.05330.0092-0.00810.03760.02560.02320.01420.07930.05540.1442-56.243-15.48543.336
20.85980.34080.14890.77830.10930.559-0.08930.18380.1473-0.11970.05990.0746-0.00580.00370.02940.0222-0.0218-0.02910.05630.05740.1337-9.8310.1318.66
30.1133-0.13140.10380.48240.03350.4719-0.00470.00830.00440.0802-0.01530.0324-0.0305-0.02760.020.0318-0.0041-0.00110.042-0.00240.1592-0.42212.75445.033
40.13540.0917-0.1630.49870.08340.5951-0.0010.00120.0117-0.1037-0.01360.0440.0123-0.0370.01460.03730.0051-0.02340.0454-0.00090.1677-46.959-28.13616.946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 465
2X-RAY DIFFRACTION2B31 - 465
3X-RAY DIFFRACTION3C31 - 465
4X-RAY DIFFRACTION4D31 - 465

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