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- PDB-8qwb: Crystal structure of citrate synthase from Methylophaga sulfidovorans -

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Basic information

Entry
Database: PDB / ID: 8qwb
TitleCrystal structure of citrate synthase from Methylophaga sulfidovorans
ComponentsCitrate synthase
KeywordsTRANSFERASE / Citrate Synthase
Function / homology
Function and homology information


citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain
Similarity search - Domain/homology
Biological speciesMethylophaga sulfidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsMais, C.-N. / Bange, G. / Sendker, F.L. / Hochberg, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Frequent evolutionary transitions in homo-oligomeric assembly across the phylogeny of bacterial citrate synthases.
Authors: Sendker, F.L. / Schlotthauer, T. / Mais, C.-N. / Lo, Y.K. / Girbig, M. / Bohn, S. / Heimerl, T. / Schindler, D. / Weinstein, A. / Metzger, B.P. / Thornton, J.W. / Pillai, A. / Bange, G. / ...Authors: Sendker, F.L. / Schlotthauer, T. / Mais, C.-N. / Lo, Y.K. / Girbig, M. / Bohn, S. / Heimerl, T. / Schindler, D. / Weinstein, A. / Metzger, B.P. / Thornton, J.W. / Pillai, A. / Bange, G. / Schuller, J.M. / Hochberg, G.K.A.
History
DepositionOct 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
D: Citrate synthase
E: Citrate synthase
F: Citrate synthase
G: Citrate synthase
H: Citrate synthase
I: Citrate synthase
J: Citrate synthase
K: Citrate synthase
L: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)537,21412
Polymers537,21412
Non-polymers00
Water00
1
A: Citrate synthase
C: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-28 kcal/mol
Surface area27580 Å2
2
B: Citrate synthase

K: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4730 Å2
ΔGint-40 kcal/mol
Surface area26690 Å2
3
D: Citrate synthase
E: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-36 kcal/mol
Surface area26270 Å2
4
F: Citrate synthase
H: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-34 kcal/mol
Surface area27060 Å2
5
G: Citrate synthase

J: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4850 Å2
ΔGint-39 kcal/mol
Surface area27170 Å2
6
I: Citrate synthase
L: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-36 kcal/mol
Surface area27180 Å2
Unit cell
Length a, b, c (Å)155.690, 96.610, 203.100
Angle α, β, γ (deg.)90.00, 110.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Citrate synthase


Mass: 44767.852 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga sulfidovorans (bacteria) / Gene: SAMN04488079_11738 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I4B681

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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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Lithium chloride, 0.1 M Citric Acid pH 5.0, 10% PEG 6000, 5mM oxaloacetic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.2→48.31 Å / Num. obs: 636593 / % possible obs: 98.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.142 / Net I/σ(I): 10.29
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.2-3.292.49967550.4312.7091
3.29-3.381.71266290.5361.8611
3.38-3.471.4564650.7221.5621
3.47-3.581.03262890.8191.1111
3.58-3.70.65560900.9230.7061
3.7-3.830.53958910.9420.5821
3.83-3.970.38756780.9680.4191
3.97-4.140.2654380.9820.2831
4.14-4.320.19952920.990.2141
4.32-4.530.15850300.9930.1711
4.53-4.770.12848010.9950.1391
4.77-5.060.10845400.9950.1161
5.06-5.410.10442650.9950.1131
5.41-5.850.09739810.9960.1051
5.85-6.410.08136920.9970.0881
6.41-7.160.06333280.9980.0691
7.16-8.270.04829480.9980.0521
8.27-10.130.04125060.9990.0441
10.13-14.320.0419440.9980.0431
14.32-48.310.04310790.9980.0471

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.201→48.31 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3245 --
Rwork0.2824 --
obs-92644 98.85 %
Refinement stepCycle: LAST / Resolution: 3.201→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30067 0 0 0 30067

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