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- PDB-3o8j: Crystal structure of 2-methylcitrate synthase (PrpC) from Salmone... -

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Basic information

Entry
Database: PDB / ID: 3o8j
TitleCrystal structure of 2-methylcitrate synthase (PrpC) from Salmonella typhimurium
Components2-methylcitrate synthase
KeywordsTRANSFERASE / Short chain fatty acids / propionate metabolism / 2-methylcitric acid cycle / PrpC or 2-MCS / GltA or CS / Citrate synthase / 2-methylcitrate synthase
Function / homology
Function and homology information


2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate metabolic process, methylcitrate cycle / citrate synthase (unknown stereospecificity) / citrate synthase activity / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytoplasm
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / 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-like, small alpha subdomain ...2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / 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-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-methylcitrate synthase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsChittori, S. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structure of Salmonella typhimurium 2-methylcitrate synthase: Insights on domain movement and substrate specificity
Authors: Chittori, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
B: 2-methylcitrate synthase
C: 2-methylcitrate synthase
D: 2-methylcitrate synthase
E: 2-methylcitrate synthase
F: 2-methylcitrate synthase
G: 2-methylcitrate synthase
H: 2-methylcitrate synthase
I: 2-methylcitrate synthase
J: 2-methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,80321
Polymers449,79010
Non-polymers1,01311
Water21,2221178
1
A: 2-methylcitrate synthase
B: 2-methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1424
Polymers89,9582
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-35 kcal/mol
Surface area26980 Å2
MethodPISA
2
C: 2-methylcitrate synthase
D: 2-methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0503
Polymers89,9582
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-27 kcal/mol
Surface area26940 Å2
MethodPISA
3
E: 2-methylcitrate synthase
F: 2-methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3266
Polymers89,9582
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-37 kcal/mol
Surface area27330 Å2
MethodPISA
4
G: 2-methylcitrate synthase
H: 2-methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1424
Polymers89,9582
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-35 kcal/mol
Surface area27100 Å2
MethodPISA
5
I: 2-methylcitrate synthase
J: 2-methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1424
Polymers89,9582
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-32 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.068, 118.159, 120.659
Angle α, β, γ (deg.)60.84, 67.77, 81.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
2-methylcitrate synthase / PrpC / Methylcitrate synthase / Citrate synthase 2


Mass: 44978.984 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: enterica serovar Typhimurium / Gene: prpC, STM0369 / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q56063, 2-methylcitrate synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1178 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Bicine, 18% PEG 4000, 1.4M ammonium sulfate, 0.2M trisodium citrate , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 6, 2008 / Details: Mirror
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 160794 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 22.17
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 4.18 / % possible all: 72.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N- (1-12) and C- terminal (361-378) deletion construct of the AbGltA (PDB: 1A59) dimer

1a59


Resolution: 2.41→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.884 / SU B: 22.088 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28247 7257 5 %RANDOM
Rwork0.21762 ---
obs0.22094 137700 91.02 %-
all-159324 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.815 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20.1 Å2
2---0.05 Å21.47 Å2
3----3.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.41→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27985 0 66 1178 29229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02128712
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.94738971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44353611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84923.4531286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.784154603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.38715191
X-RAY DIFFRACTIONr_chiral_restr0.0840.24303
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02121887
X-RAY DIFFRACTIONr_mcbond_it0.4111.517992
X-RAY DIFFRACTIONr_mcangle_it0.762228869
X-RAY DIFFRACTIONr_scbond_it1.086310720
X-RAY DIFFRACTIONr_scangle_it1.7514.510102
LS refinement shellResolution: 2.406→2.469 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 438 -
Rwork0.24 8698 -
obs--77.57 %
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)
10.68090.0376-0.0780.4690.18530.58110.00420.03540.0545-0.06630.0227-0.09340.01040.0839-0.02690.0166-0.00140.02830.0275-0.0050.0718-39.0331-65.9082-79.342
20.5838-0.078-0.06960.3840.08070.94230.03430.0861-0.0452-0.0945-0.05320.0132-0.0161-0.17620.01880.02530.01090.00080.0524-0.02770.0618-69.3846-73.8132-81.534
30.70520.03070.0960.5579-0.07370.75480.01130.0065-0.02730.0737-0.0042-0.11440.15770.3239-0.00710.04790.0724-0.01690.1453-0.01350.0649-26.7913-82.5697-40.4181
40.63830.0580.0510.76060.14910.84140.0080.0519-0.10060.0137-0.0027-0.02640.34290.019-0.00530.1550.00190.00140.0072-0.01020.0593-52.4305-99.1818-50.1646
50.45460.16840.06760.6681-0.04030.7112-0.0173-0.0802-0.00210.1203-0.0018-0.0725-0.06930.05930.01910.0320.0025-0.02030.0240.0020.0325-43.4502-56.6706-8.8096
60.49940.04710.13930.7006-0.09110.67270.0008-0.0483-0.07240.09860.01630.08540.1435-0.0123-0.0170.05430.00390.01720.00940.02050.0505-62.7562-81.1714-11.2173
70.6408-0.0935-0.06480.58810.12210.79290.0057-0.02960.12-0.02030.0161-0.0377-0.2069-0.0144-0.02180.05780.00240.00770.0039-0.00560.048-64.7795-23.7861-27.7793
80.5362-0.0665-0.01680.43740.13830.6209-0.0284-0.02390.00210.0766-0.02360.08070.0084-0.13650.0520.01640.00250.02380.03390.00080.0739-86.1579-44.9345-18.7477
90.3898-0.02690.14320.5449-0.04610.73430.0130.08040.0814-0.0691-0.0296-0.0177-0.15570.07180.01660.0507-0.0030.01610.0210.02250.0599-62.3173-29.5171-71.7214
100.67550.0108-0.01050.6376-0.11180.5925-0.00580.00190.00910.02820.02740.1454-0.1474-0.209-0.02160.03810.04920.00980.0813-0.00110.0674-90.5197-40.3252-62.855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 389
2X-RAY DIFFRACTION2B26 - 389
3X-RAY DIFFRACTION3C26 - 388
4X-RAY DIFFRACTION4D28 - 389
5X-RAY DIFFRACTION5E26 - 389
6X-RAY DIFFRACTION6F26 - 389
7X-RAY DIFFRACTION7G26 - 389
8X-RAY DIFFRACTION8H28 - 389
9X-RAY DIFFRACTION9I28 - 389
10X-RAY DIFFRACTION10J26 - 389

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