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- PDB-8hgn: Crystal structure of MeaC (Mesaconyl-CoA hydratase) -

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Basic information

Entry
Database: PDB / ID: 8hgn
TitleCrystal structure of MeaC (Mesaconyl-CoA hydratase)
ComponentsBeta-methylmalyl-CoA dehydratase
KeywordsLYASE
Function / homology: / Mesaconyl-CoA hydratase / Thiol ester hydratase, Rv0216, predicted / : / HotDog domain superfamily / lyase activity / D-MALATE / MaoC domain protein dehydratase
Function and homology information
Biological speciesMethylorubrum extorquens CM4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAhn, J.W. / Hong, J. / Kim, K.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Microbiol Biotechnol. / Year: 2023
Title: Crystal Structure of Mesaconyl-CoA Hydratase from Methylorubrum extorquens CM4.
Authors: Ahn, J.W. / Hong, J. / Kim, K.J.
History
DepositionNov 15, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-methylmalyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9862
Polymers38,8521
Non-polymers1341
Water1,62190
1
A: Beta-methylmalyl-CoA dehydratase
hetero molecules

A: Beta-methylmalyl-CoA dehydratase
hetero molecules

A: Beta-methylmalyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9576
Polymers116,5553
Non-polymers4023
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area10120 Å2
ΔGint-40 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.224, 79.224, 91.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Beta-methylmalyl-CoA dehydratase / 2-methylfumaryl-CoA hydratase / Mesaconyl-CoA hydratase


Mass: 38851.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens CM4 (bacteria)
Strain: CM4 / NCIMB 13688 / Gene: Mchl_4075 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7KZU4
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20%(w/v) PEG3350, 0.2M DL-Malic acid (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 23337 / % possible obs: 98.5 % / Redundancy: 6.9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.039 / Rrim(I) all: 0.115 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.95-1.982.20.20920484.715185.4
1.98-2.022.70.2221175.002193.1
2.02-2.0630.21221955.654194.2
2.06-2.130.20521786.692193.6
2.1-2.1530.19221796.91193.7
2.15-2.23.20.18522107.451193.7
2.2-2.253.20.18121598.258193.7
2.25-2.313.30.17121538.064192.7
2.31-2.383.30.16521948.372193.7
2.38-2.463.40.15821879.181193.3
2.46-2.543.50.148216810.343193
2.54-2.653.60.13921849.995194.1
2.65-2.773.80.134215811.351193.7
2.77-2.9140.128223412.612195.3
2.91-3.14.10.115225313.27196.7
3.1-3.334.30.106229713.526198.7
3.33-3.674.60.1232515.224199.5
3.67-4.24.80.091233314.464199.7
4.2-5.294.90.079232712.279199.7
5.29-504.70.07922739.248197.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E3E

4e3e


Resolution: 1.95→32.12 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.759 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27811 1180 5.1 %RANDOM
Rwork0.20983 ---
obs0.21341 22150 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.885 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å2-0 Å2
2---0.46 Å20 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.95→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 9 90 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132796
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152589
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.6463809
X-RAY DIFFRACTIONr_angle_other_deg1.2681.5765949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0415352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83121.081148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.731521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9353.4241411
X-RAY DIFFRACTIONr_mcbond_other2.9163.4231410
X-RAY DIFFRACTIONr_mcangle_it4.0045.1341762
X-RAY DIFFRACTIONr_mcangle_other4.0045.1351763
X-RAY DIFFRACTIONr_scbond_it2.8453.6561385
X-RAY DIFFRACTIONr_scbond_other2.8463.6561384
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2435.3942048
X-RAY DIFFRACTIONr_long_range_B_refined6.02338.9672937
X-RAY DIFFRACTIONr_long_range_B_other6.02238.9722931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 86 -
Rwork0.282 1573 -
obs--94.96 %

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