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- PDB-8apr: CaMct - Mesaconyl-CoA C1:C4 CoA Transferase of Chloroflexus auran... -

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Basic information

Entry
Database: PDB / ID: 8apr
TitleCaMct - Mesaconyl-CoA C1:C4 CoA Transferase of Chloroflexus aurantiacus
Components2-methylfumaryl-CoA isomerase
KeywordsTRANSFERASE / mesaconyl-CoA / methylfumaryl-CoA / isomerase / intramolecular / methylfumaryl-CoA isomerase / 3-Hydroxypropionate / 3OHP
Function / homology2-methylfumaryl-CoA isomerase / intramolecular acyltransferase activity / Mesaconyl-CoA isomerase / carbon fixation by 3-hydroxypropionate cycle / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / 2-methylfumaryl-CoA isomerase
Function and homology information
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPfister, P. / Zarzycki, J. / Erb, T.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Biochemistry / Year: 2023
Title: Structural Basis for a Cork-Up Mechanism of the Intra-Molecular Mesaconyl-CoA Transferase.
Authors: Pfister, P. / Zarzycki, J. / Erb, T.J.
History
DepositionAug 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-methylfumaryl-CoA isomerase
B: 2-methylfumaryl-CoA isomerase
C: 2-methylfumaryl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3136
Polymers142,2073
Non-polymers1063
Water9,530529
1
A: 2-methylfumaryl-CoA isomerase
B: 2-methylfumaryl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8754
Polymers94,8042
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-123 kcal/mol
Surface area29040 Å2
MethodPISA
2
C: 2-methylfumaryl-CoA isomerase
hetero molecules

C: 2-methylfumaryl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8754
Polymers94,8042
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13450 Å2
ΔGint-124 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.600, 103.520, 95.300
Angle α, β, γ (deg.)90.000, 119.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-methylfumaryl-CoA isomerase


Mass: 47402.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus J-10-fl (bacteria)
Strain: ATCC 29366 / DSM 635 / J-10-fl / Gene: mct, Caur_0175 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9WC36, 2-methylfumaryl-CoA isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.73 % / Description: needles
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 200 mM Sodium chloride, 100 mM Sodium potassium phosphate pH 6.2, 50% v/v Polyethylene glycol 200

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96862 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.1→29.53 Å / Num. obs: 84090 / % possible obs: 99.4 % / Redundancy: 6.853 % / Biso Wilson estimate: 35.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.11 / Χ2: 0.893 / Net I/σ(I): 13.47 / Num. measured all: 576267 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.166.2290.8982.237211620659740.8580.98196.3
2.16-2.226.7840.82.6841075607060550.8910.86799.8
2.22-2.287.1290.6583.4242215593259220.9210.7199.8
2.28-2.357.0860.5274.1440345571556940.9460.56999.6
2.35-2.437.0510.4754.6339204557755600.9510.51399.7
2.43-2.527.0550.3785.8338015540953880.9680.40899.6
2.52-2.616.9270.3057.0335697516051530.9740.3399.9
2.61-2.726.610.248.2533175504250190.9830.26199.5
2.72-2.846.4730.19510.130771476647540.9830.21399.7
2.84-2.987.2110.16112.5833156461645980.9920.17499.6
2.98-3.147.230.12415.6831467436343520.9950.13499.7
3.14-3.337.1090.119.1629280413341190.9960.10899.7
3.33-3.566.9560.07922.9726963388938760.9970.08699.7
3.56-3.846.6020.06526.1423924363836240.9970.07199.6
3.84-4.216.080.05129.5620259335433320.9980.05699.3
4.21-4.717.0630.04734.2321294302730150.9980.05199.6
4.71-5.437.0440.04435.1218780267526660.9990.04799.7
5.43-6.656.7910.04434.1415416228422700.9990.04799.4
6.65-9.416.3240.03439.4711150177417630.9990.03799.4
9.41-29.537.1860.02747.63687010049560.9990.02995.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ubm

3ubm


Resolution: 2.1→29.53 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 1999 2.38 %
Rwork0.18 82023 -
obs0.1808 84022 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.89 Å2 / Biso mean: 41.8278 Å2 / Biso min: 29.28 Å2
Refinement stepCycle: final / Resolution: 2.1→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9354 0 3 529 9886
Biso mean--41.6 44.28 -
Num. residues----1212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.32881420.27495602574496
2.16-2.220.29721330.244858305963100
2.22-2.280.24391420.221358726014100
2.28-2.350.26261510.258155966100
2.35-2.440.25081390.19358796018100
2.44-2.540.23361420.184258475989100
2.54-2.650.24311450.181558926037100
2.65-2.790.21971420.184658415983100
2.79-2.970.21761500.185258636013100
2.97-3.190.24381400.183858866026100
3.19-3.510.20111350.179658966031100
3.52-4.020.19621480.168559016049100
4.02-5.060.1631410.154759076048100
5.06-29.530.19761490.17359926141100
Refinement TLS params.Method: refined / Origin x: 13.8375 Å / Origin y: 81.9542 Å / Origin z: 15.0757 Å
111213212223313233
T0.3862 Å2-0.0012 Å2-0.1166 Å2-0.3492 Å20.0027 Å2--0.371 Å2
L0.2318 °20.0694 °20.0501 °2-0.2808 °20.057 °2--0.2127 °2
S0.022 Å °-0.0368 Å °0.004 Å °0.0487 Å °-0.0193 Å °-0.0506 Å °0.0188 Å °0.032 Å °-0.007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 450
2X-RAY DIFFRACTION1allB2 - 450
3X-RAY DIFFRACTION1allC2 - 450
4X-RAY DIFFRACTION1allS1 - 538

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