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

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Basic information

Entry
Database: PDB / ID: 8apq
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 / homology
Function and homology information


2-methylfumaryl-CoA isomerase / intramolecular acyltransferase activity / carbon fixation by 3-hydroxypropionate cycle
Similarity search - Function
Mesaconyl-CoA isomerase / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III
Similarity search - Domain/homology
COENZYME A / (2E)-2-METHYLBUT-2-ENEDIOIC ACID / Mesaconyl Coenzme A / 2-methylfumaryl-CoA isomerase
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)289,78117
Polymers284,4136
Non-polymers5,36811
Water19,0061055
1
A: 2-methylfumaryl-CoA isomerase
B: 2-methylfumaryl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5825
Polymers94,8042
Non-polymers1,7773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-93 kcal/mol
Surface area28070 Å2
MethodPISA
2
C: 2-methylfumaryl-CoA isomerase
D: 2-methylfumaryl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6006
Polymers94,8042
Non-polymers1,7954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17000 Å2
ΔGint-91 kcal/mol
Surface area27860 Å2
MethodPISA
3
E: 2-methylfumaryl-CoA isomerase
F: 2-methylfumaryl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6006
Polymers94,8042
Non-polymers1,7954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16930 Å2
ΔGint-86 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.840, 193.840, 251.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
2-methylfumaryl-CoA isomerase


Mass: 47402.195 Da / Num. of mol.: 6
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-OA9 / Mesaconyl Coenzme A / (~{E})-4-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-methyl-4-oxidanylidene-but-2-enoic acid / Mesaconyl-CoA / 2-methylfumaroyl-CoA


Mass: 879.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H40N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MEZ / (2E)-2-METHYLBUT-2-ENEDIOIC ACID / MESACONIC ACID / MESACONATE


Mass: 130.099 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1055 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

CrystalDescription: needles
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 35% 2-Methyl-2,4-pentanediol, 100 mM Sodium/potassium phosphate pH 6.2

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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: P14 (MX2) / Wavelength: 0.9766 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 2.49→29.69 Å / Num. obs: 189902 / % possible obs: 99.7 % / Redundancy: 5.849 % / Biso Wilson estimate: 47.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.098 / Χ2: 0.899 / Net I/σ(I): 13.57 / Num. measured all: 1110756 / Scaling rejects: 23
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
2.49-2.565.9570.7332.588240713945138340.7870.80399.2
2.56-2.635.9220.6013.128087713672136560.850.65899.9
2.63-2.75.8980.5143.617785613209132000.8850.56399.9
2.7-2.795.890.4084.427599112908129010.9240.44799.9
2.79-2.885.8830.3215.517317912476124390.9520.35299.7
2.88-2.985.9490.2526.797180212116120690.9690.27699.6
2.98-3.095.9750.1918.786976811681116770.9820.209100
3.09-3.225.9760.14910.96697811216112070.9890.16399.9
3.22-3.365.9120.12112.926394810825108170.9920.13299.9
3.36-3.525.8620.09715.686058310343103350.9950.10699.9
3.52-3.715.8220.08218.0557133981998130.9960.0999.9
3.71-3.945.7560.06921.1353504930992950.9960.07699.8
3.94-4.215.720.0623.9649955876787330.9970.06699.6
4.21-4.555.6670.05426.1746041816481240.9970.0699.5
4.55-4.985.8230.05127.5244043757075630.9970.05699.9
4.98-5.575.8410.05127.2439878683768270.9980.05699.9
5.57-6.435.7670.05326.3935030608160740.9980.05899.9
6.43-7.885.5990.04629.3328759515851360.9980.0599.6
7.88-11.145.520.03834.6522186405040190.9990.04299.2
11.14-29.694.9650.03635.0910838234321830.9990.0493.2

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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: 2.49→29.69 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 1998 1.05 %
Rwork0.185 187873 -
obs0.1852 189871 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.74 Å2 / Biso mean: 50.5406 Å2 / Biso min: 33.37 Å2
Refinement stepCycle: final / Resolution: 2.49→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18795 0 337 1055 20187
Biso mean--68.48 50.19 -
Num. residues----2435
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 (%)
2.49-2.550.27041410.2406132301337199
2.55-2.620.25891420.22651332113463100
2.62-2.70.25411410.23341334113482100
2.7-2.790.23071420.21361333513477100
2.79-2.890.2461450.21391331813463100
2.89-30.26551390.20231335713496100
3-3.140.25551420.20161337313515100
3.14-3.30.20131440.18771338613530100
3.3-3.510.2121410.18861338013521100
3.51-3.780.18751440.17571346613610100
3.78-4.160.16611430.15681341513558100
4.16-4.760.14071440.14791349213636100
4.76-5.990.17131410.17371359813739100
5.99-29.690.21021490.2007138611401099
Refinement TLS params.Method: refined / Origin x: -80.6723 Å / Origin y: 40.4872 Å / Origin z: 33.557 Å
111213212223313233
T0.3461 Å20.0022 Å20.0144 Å2-0.3216 Å20.0249 Å2--0.2985 Å2
L0.1471 °2-0.0882 °20.0763 °2-0.1924 °2-0.0368 °2--0.3801 °2
S0.0429 Å °-0.0248 Å °-0.0222 Å °-0.0483 Å °0.0126 Å °0.011 Å °0.0405 Å °0.0054 Å °-0.0546 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 500
2X-RAY DIFFRACTION1allB1 - 510
3X-RAY DIFFRACTION1allC1 - 510
4X-RAY DIFFRACTION1allD1 - 510
5X-RAY DIFFRACTION1allE2 - 510
6X-RAY DIFFRACTION1allF1 - 500
7X-RAY DIFFRACTION1allF510
8X-RAY DIFFRACTION1allS1 - 1055

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