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

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Basic information

Entry
Database: PDB / ID: 5uqr
TitleCrystal structure of 2-methylcitrate synthase from Aspergillus fumigatus
Components2-methylcitrate synthase, mitochondrial
KeywordsTRANSFERASE / mcsA / 2-methylcitrate synthase / citrate synthase / ethyl-CoA / oxaloacetate
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
Chem-8JD / OXALOACETATE ION / 2-methylcitrate synthase, mitochondrial
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.0Mar 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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)98,1628
Polymers97,1152
Non-polymers1,0476
Water23,2031288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-76 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.724, 94.110, 124.404
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: 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: 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 1


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


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-8JD / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name) / Ethyl Coenzyme A


Mass: 715.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H39N7O13P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1288 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.15 M DL-Malic Acid pH 7.0, 20% PEG3350

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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: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 77525 / % possible obs: 98.12 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.041 / Rrim(I) all: 0.104 / Rsym value: 0.078 / Net I/σ(I): 16.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 3801 / CC1/2: 0.722 / Rpim(I) all: 0.303 / Rrim(I) all: 0.634 / Rsym value: 0.529 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→31.11 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17529 4085 5 %RANDOM
Rwork0.14204 ---
obs0.14372 77525 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.701 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.36 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.75→31.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6802 0 67 1288 8157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197048
X-RAY DIFFRACTIONr_bond_other_d00.026623
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.989566
X-RAY DIFFRACTIONr_angle_other_deg3.585315387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3445876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02924.133300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.827151188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7081538
X-RAY DIFFRACTIONr_chiral_restr0.0890.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217809
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021394
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_it0.8311.2963504
X-RAY DIFFRACTIONr_mcbond_other0.8311.2953503
X-RAY DIFFRACTIONr_mcangle_it1.4341.9394380
X-RAY DIFFRACTIONr_mcangle_other1.4341.944381
X-RAY DIFFRACTIONr_scbond_it1.1261.4713544
X-RAY DIFFRACTIONr_scbond_other1.1261.4713545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9152.1285187
X-RAY DIFFRACTIONr_long_range_B_refined4.65317.9158812
X-RAY DIFFRACTIONr_long_range_B_other4.65317.9158813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27914 / 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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 264 -
Rwork0.22 5423 -
obs--94.05 %
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)
10.54480.24840.38690.90220.67640.74320.0258-0.0694-0.04310.07750.0277-0.06830.0849-0.0036-0.05360.01570.0026-0.00710.01430.00390.01229.346-35.852-12.89
20.1405-0.0016-0.1010.13570.04270.1914-0.0099-0.00930.00430.01260.02250.0185-0.01070.0118-0.01250.00870.00420.0010.0087-0.00040.032218.851-17.451-17.633
30.87880.62730.77131.50481.53931.6048-0.08990.02850.0958-0.1497-0.18250.2693-0.1562-0.16670.27250.03990.0171-0.03840.0423-0.03870.056-12.406-28.939-19.466
40.18430.0192-0.03870.05040.1140.3014-0.0198-0.01960.00210.005-0.01440.00950.0242-0.02640.03420.0217-0.00050.00210.0059-0.00040.04046.153-29.385-16.497
50.70360.10910.73680.7515-0.28521.0270.0575-0.0841-0.0453-0.00240.01480.12170.0696-0.1515-0.07230.0126-0.0182-0.0050.0781-0.04390.08017.435-48.297-43.323
60.0922-0.0140.02820.24150.08530.16720.00270.0147-0.0043-0.0417-0.01320.0207-0.0047-0.00740.01040.01130.0018-0.00860.0099-0.00440.025422.894-30.574-45.547
70.1272-0.0515-0.03280.24250.06650.0674-0.00270.00990.0056-0.0280.0088-0.02270.01260.0181-0.00620.016-0.00180.00150.0206-0.00260.016938.229-34.593-41.308
84.0032-2.60972.9451.9966-0.75916.8358-0.0262-0.2053-0.02140.10510.1619-0.01010.3797-0.0109-0.13570.05540.0216-0.02290.02670.00570.037827.204-41.369-8.317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 77
2X-RAY DIFFRACTION2A78 - 309
3X-RAY DIFFRACTION3A310 - 345
4X-RAY DIFFRACTION4A346 - 465
5X-RAY DIFFRACTION5B31 - 59
6X-RAY DIFFRACTION6B60 - 326
7X-RAY DIFFRACTION7B327 - 457
8X-RAY DIFFRACTION8B458 - 465

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