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- PDB-4l9y: Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in c... -

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Basic information

Entry
Database: PDB / ID: 4l9y
TitleCrystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, glyoxylate, and propionyl-CoA
ComponentsMalyl-CoA lyase
KeywordsLYASE / TIM barrel
Function / homology
Function and homology information


malyl-CoA lyase / L-erythro-3-methylmalyl-CoA lyase activity / malyl-CoA lyase activity / (S)-citramalyl-CoA lyase / (S)-citramalyl-CoA lyase activity / oxaloacetate metabolic process / magnesium ion binding / metal ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / 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
propionyl Coenzyme A / GLYOXYLIC ACID / L-malyl-CoA/beta-methylmalyl-CoA lyase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 Å
AuthorsZarzycki, J. / Kerfeld, C.A.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases.
Authors: Zarzycki, J. / Kerfeld, C.A.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malyl-CoA lyase
B: Malyl-CoA lyase
C: Malyl-CoA lyase
D: Malyl-CoA lyase
E: Malyl-CoA lyase
F: Malyl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,41719
Polymers221,1586
Non-polymers1,25913
Water28,2661569
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27470 Å2
ΔGint-254 kcal/mol
Surface area57040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.210, 143.995, 94.221
Angle α, β, γ (deg.)90.000, 112.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Malyl-CoA lyase / (3S)-malyl-CoA/beta-methylmalyl-CoA lyase / L-malyl-CoA/beta-methylmalyl-CoA lyase


Mass: 36859.684 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: mcl1, RHOS4_03500, RSP_1771 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3J5L6, malyl-CoA lyase

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Non-polymers , 5 types, 1582 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O17P3S
#5: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1569 / 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: 2.43 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 parts protein solution (3.0 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 3 parts buffer (0.1 M Tris-HCl, pH 8.5, 20% w/v PEG3350, 20 mM magnesium ...Details: 2 parts protein solution (3.0 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 3 parts buffer (0.1 M Tris-HCl, pH 8.5, 20% w/v PEG3350, 20 mM magnesium chloride), crystals soaked in crystallization mixture + 8 mM propionyl-CoA + 25% v/v glycerol for 3 minutes before plunging into liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.102→38.791 Å / Num. all: 113853 / Num. obs: 113853 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rsym value: 0.066 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.102-2.223.80.4481.761474163640.44898.2
2.22-2.353.80.312.559990157690.3199.9
2.35-2.513.80.2213.556303147920.22199.9
2.51-2.713.80.1515.152362137640.15199.9
2.71-2.973.80.0997.748210127020.09999.9
2.97-3.323.80.0612.743200114650.0699.9
3.32-3.843.70.03918.537592101260.03999.7
3.84-4.73.70.02824.33141885680.02899.7
4.7-6.653.70.02526.82423266270.02599.7
6.65-38.7913.70.01932.41366936760.01999.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.8.2_1303refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U5H

1u5h


Resolution: 2.102→38.791 Å / Occupancy max: 1 / Occupancy min: 0.76 / SU ML: 0.24 / σ(F): 1.36 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 1998 1.76 %
Rwork0.1769 --
obs0.1774 113793 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.67 Å2 / Biso mean: 23.5469 Å2 / Biso min: 5.91 Å2
Refinement stepCycle: LAST / Resolution: 2.102→38.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13166 0 72 1569 14807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313519
X-RAY DIFFRACTIONf_angle_d0.74618371
X-RAY DIFFRACTIONf_chiral_restr0.0542007
X-RAY DIFFRACTIONf_plane_restr0.0032435
X-RAY DIFFRACTIONf_dihedral_angle_d12.4374913
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.102-2.12760.30741500.28677079722990
2.1276-2.15460.27981180.268780398157100
2.1546-2.18290.31751440.2678908034100
2.1829-2.21280.28231330.248379278060100
2.2128-2.24440.2731580.238779238081100
2.2444-2.27790.28441470.237178578004100
2.2779-2.31350.27571250.228779498074100
2.3135-2.35140.24831550.22479368091100
2.3514-2.3920.25321180.220479068024100
2.392-2.43550.25861650.217778698034100
2.4355-2.48230.26051420.203179308072100
2.4823-2.5330.25791500.203278377987100
2.533-2.5880.20141310.203379158046100
2.588-2.64820.20721410.19427929807099
2.6482-2.71440.30891390.193478597998100
2.7144-2.78780.24441470.191979438090100
2.7878-2.86980.19831420.188478868028100
2.8698-2.96240.23481290.18097934806399
2.9624-3.06830.18441520.17557842799499
3.0683-3.19110.18461500.17067865801599
3.1911-3.33620.19061380.16047876801499
3.3362-3.5120.19361400.16077938807899
3.512-3.73190.15641470.14857846799399
3.7319-4.01970.17071390.13647901804099
4.0197-4.42370.16661310.1367849798099
4.4237-5.06270.1721360.13617853798999
5.0627-6.37380.15871390.15697906804599
6.3738-38.79750.19491440.166578978041100

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