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- PDB-5ugr: Malyl-CoA lyase from Methylobacterium extorquens -

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Basic information

Entry
Database: PDB / ID: 5ugr
TitleMalyl-CoA lyase from Methylobacterium extorquens
ComponentsMalyl-CoA lyase/beta-methylmalyl-CoA lyase
KeywordsLYASE
Function / homology
Function and homology information


malyl-CoA lyase / L-erythro-3-methylmalyl-CoA lyase activity / malyl-CoA lyase activity / metal ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Malyl-CoA lyase/beta-methylmalyl-CoA lyase
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsGonzalez, J.M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift.
Authors: Gonzalez, J.M. / Marti-Arbona, R. / Chen, J.C. / Unkefer, C.J.
History
DepositionJan 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
SupersessionAug 23, 2017ID: 4ROQ
Revision 1.2Aug 23, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_database_PDB_obs_spr / Item: _diffrn_detector.detector
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malyl-CoA lyase/beta-methylmalyl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0264
Polymers36,7281
Non-polymers2983
Water7,026390
1
A: Malyl-CoA lyase/beta-methylmalyl-CoA lyase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)222,15424
Polymers220,3666
Non-polymers1,78818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_668-y+1,-x+1,-z+31
crystal symmetry operation11_558-x+y,y,-z+31
crystal symmetry operation12_568x,x-y+1,-z+31
Buried area34270 Å2
ΔGint-267 kcal/mol
Surface area68490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.524, 126.524, 103.207
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-697-

HOH

21A-701-

HOH

31A-742-

HOH

41A-769-

HOH

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Components

#1: Protein Malyl-CoA lyase/beta-methylmalyl-CoA lyase


Mass: 36727.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: mcl, MexAM1_META1p1733 / Production host: Escherichia coli (E. coli) / References: UniProt: C5B113, malyl-CoA lyase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes, pH 7.5, 30 % w/v PEG 400, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127092 Å / Relative weight: 1
ReflectionResolution: 1.56→38.44 Å / Num. obs: 62486 / % possible obs: 91.1 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2% possible all
1.56-1.595.90.5222.726420.84579.3
8.55-38.4411.40.031623980.99880.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L9Z

4l9z


Resolution: 1.56→38.44 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.75 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13422 3059 4.9 %RANDOM
Rwork0.10219 ---
obs0.10375 59427 90.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 1.56→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 18 390 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192629
X-RAY DIFFRACTIONr_bond_other_d0.0020.022570
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9693559
X-RAY DIFFRACTIONr_angle_other_deg1.2235906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32323.644118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0161525
X-RAY DIFFRACTIONr_chiral_restr0.1180.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213002
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02583
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_it2.341.8041324
X-RAY DIFFRACTIONr_mcbond_other2.2321.7991323
X-RAY DIFFRACTIONr_mcangle_it2.6642.7131663
X-RAY DIFFRACTIONr_mcangle_other2.7042.7171664
X-RAY DIFFRACTIONr_scbond_it3.7262.1631305
X-RAY DIFFRACTIONr_scbond_other3.7252.1631306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1189.4121888
X-RAY DIFFRACTIONr_long_range_B_refined4.28316.5223299
X-RAY DIFFRACTIONr_long_range_B_other3.80915.5213091
X-RAY DIFFRACTIONr_rigid_bond_restr7.17635195
X-RAY DIFFRACTIONr_sphericity_free31.261593
X-RAY DIFFRACTIONr_sphericity_bonded10.73655437
LS refinement shellResolution: 1.562→1.602 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.188 207 -
Rwork0.162 3979 -
obs--83.37 %

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