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- PDB-7xkg: Crystal structure of an intramolecular mesacyl-CoA transferase fr... -

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Basic information

Entry
Database: PDB / ID: 7xkg
TitleCrystal structure of an intramolecular mesacyl-CoA transferase from the 3-hydroxypropionic acid cycle of Roseiflexus castenholzii
ComponentsAcyl-CoA transferase/carnitine dehydratase-like protein
KeywordsTRANSFERASE
Function / homologyMesaconyl-CoA isomerase / : / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / transferase activity / Acyl-CoA transferase/carnitine dehydratase-like protein
Function and homology information
Biological speciesRoseiflexus castenholzii DSM 13941 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.5 Å
AuthorsMin, Z.Z. / Fan, C.P. / Wu, W.P. / Xin, Y.Y. / Liu, M.H. / Zhang, X. / Wang, Z.G. / Xu, X.L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171227 China
National Natural Science Foundation of China (NSFC)31870740 China
National Natural Science Foundation of China (NSFC)31570738 China
CitationJournal: Front Microbiol / Year: 2022
Title: Crystal Structure of an Intramolecular Mesaconyl-Coenzyme A Transferase From the 3-Hydroxypropionic Acid Cycle of Roseiflexus castenholzii .
Authors: Min, Z. / Zhang, X. / Wu, W. / Xin, Y. / Liu, M. / Wang, K. / Zhang, X. / He, Y. / Fan, C. / Wang, Z. / Xu, X.
History
DepositionApr 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA transferase/carnitine dehydratase-like protein
B: Acyl-CoA transferase/carnitine dehydratase-like protein
C: Acyl-CoA transferase/carnitine dehydratase-like protein
D: Acyl-CoA transferase/carnitine dehydratase-like protein
E: Acyl-CoA transferase/carnitine dehydratase-like protein
F: Acyl-CoA transferase/carnitine dehydratase-like protein


Theoretical massNumber of molelcules
Total (without water)283,2786
Polymers283,2786
Non-polymers00
Water31,4541746
1
A: Acyl-CoA transferase/carnitine dehydratase-like protein
B: Acyl-CoA transferase/carnitine dehydratase-like protein


Theoretical massNumber of molelcules
Total (without water)94,4262
Polymers94,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-95 kcal/mol
Surface area29010 Å2
MethodPISA
2
C: Acyl-CoA transferase/carnitine dehydratase-like protein
D: Acyl-CoA transferase/carnitine dehydratase-like protein


Theoretical massNumber of molelcules
Total (without water)94,4262
Polymers94,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-93 kcal/mol
Surface area28770 Å2
MethodPISA
3
E: Acyl-CoA transferase/carnitine dehydratase-like protein
F: Acyl-CoA transferase/carnitine dehydratase-like protein


Theoretical massNumber of molelcules
Total (without water)94,4262
Polymers94,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-94 kcal/mol
Surface area29200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)364.413, 210.118, 73.476
Angle α, β, γ (deg.)90.000, 95.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Acyl-CoA transferase/carnitine dehydratase-like protein


Mass: 47213.035 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseiflexus castenholzii DSM 13941 (bacteria)
Strain: DSM 13941 / HLO8 / Gene: Rcas_0911 / Details (production host): pEASY-E1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7NHS9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1746 / 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: 5.2 Å3/Da / Density % sol: 76.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14 % PEG4000, 0.1 M Sodium Citrate, 0.1 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CCD / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 188922 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.43 Å2 / CC1/2: 0.956 / CC star: 0.989 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.059 / Rrim(I) all: 0.156 / Net I/σ(I): 15.82
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.95 / Num. unique obs: 9443 / CC1/2: 0.902 / CC star: 0.974 / Rpim(I) all: 0.189 / Rrim(I) all: 0.492 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot3.27model building
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.5→44.42 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 9367 4.97 %
Rwork0.1587 178955 -
obs0.1604 188322 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.85 Å2 / Biso mean: 30.5313 Å2 / Biso min: 12.28 Å2
Refinement stepCycle: final / Resolution: 2.5→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18792 0 0 1746 20538
Biso mean---34.39 -
Num. residues----2435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.530.25772790.19525517579691
2.53-2.560.23193000.176859366236100
2.56-2.590.21572710.172860766347100
2.59-2.620.22082860.172160836369100
2.62-2.650.21663180.175858936211100
2.65-2.690.21253200.181259936313100
2.69-2.730.24393280.181760546382100
2.73-2.770.22753190.17065882620199
2.77-2.810.20232920.16475977626999
2.81-2.860.19743330.1659506283100
2.86-2.910.19253050.159659746279100
2.91-2.960.21613060.170460836389100
2.96-3.020.21523310.173159156246100
3.02-3.080.24143110.175560286339100
3.08-3.150.19572780.170660486326100
3.15-3.220.20393190.1659966315100
3.22-3.30.20312860.167460246310100
3.3-3.390.21563390.172860076346100
3.39-3.490.19092970.161760226319100
3.49-3.60.18663060.15965955626199
3.6-3.730.20853160.15985957627399
3.73-3.880.17133100.141960666376100
3.88-4.060.16283350.141259516286100
4.06-4.270.16153230.133959896312100
4.27-4.540.15963480.131759746322100
4.54-4.890.16523320.138960066338100
4.89-5.380.16483370.14585918625599
5.38-6.150.20682950.164860866381100
6.15-7.740.20053200.17265990631099
7.75-44.420.16063270.15295605593292

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