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- PDB-4lhp: Crystal Structure of Native FG41Malonate Semialdehyde Decarboxylase -

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Basic information

Entry
Database: PDB / ID: 4lhp
TitleCrystal Structure of Native FG41Malonate Semialdehyde Decarboxylase
ComponentsFG41 Malonate Semialdehyde Decarboxylase
KeywordsISOMERASE / The tautomerase Superfamily / beta-alpha-beta-motif
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases
Similarity search - Function
Tautomerase, MSAD family / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / FG41 Malonate Semialdehyde Decarboxylase
Similarity search - Component
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsGuo, Y. / Serrano, H. / Poelarends, G.J. / Johnson Jr., W.H. / Hackert, M.L. / Whitman, C.P.
CitationJournal: Biochemistry / Year: 2013
Title: Kinetic, Mutational, and Structural Analysis of Malonate Semialdehyde Decarboxylase from Coryneform Bacterium Strain FG41: Mechanistic Implications for the Decarboxylase and Hydratase Activities.
Authors: Guo, Y. / Serrano, H. / Poelarends, G.J. / Johnson, W.H. / Hackert, M.L. / Whitman, C.P.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 26, 2014Group: Other
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FG41 Malonate Semialdehyde Decarboxylase
B: FG41 Malonate Semialdehyde Decarboxylase
C: FG41 Malonate Semialdehyde Decarboxylase
D: FG41 Malonate Semialdehyde Decarboxylase
E: FG41 Malonate Semialdehyde Decarboxylase
F: FG41 Malonate Semialdehyde Decarboxylase
G: FG41 Malonate Semialdehyde Decarboxylase
H: FG41 Malonate Semialdehyde Decarboxylase
I: FG41 Malonate Semialdehyde Decarboxylase
J: FG41 Malonate Semialdehyde Decarboxylase
K: FG41 Malonate Semialdehyde Decarboxylase
L: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,08026
Polymers174,74812
Non-polymers1,33214
Water21,1321173
1
A: FG41 Malonate Semialdehyde Decarboxylase
B: FG41 Malonate Semialdehyde Decarboxylase
C: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9726
Polymers43,6873
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-68 kcal/mol
Surface area13590 Å2
MethodPISA
2
D: FG41 Malonate Semialdehyde Decarboxylase
E: FG41 Malonate Semialdehyde Decarboxylase
F: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1648
Polymers43,6873
Non-polymers4775
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-99 kcal/mol
Surface area13710 Å2
MethodPISA
3
G: FG41 Malonate Semialdehyde Decarboxylase
H: FG41 Malonate Semialdehyde Decarboxylase
I: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9726
Polymers43,6873
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-71 kcal/mol
Surface area13420 Å2
MethodPISA
4
J: FG41 Malonate Semialdehyde Decarboxylase
K: FG41 Malonate Semialdehyde Decarboxylase
L: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9726
Polymers43,6873
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-69 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.955, 94.692, 190.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
FG41 Malonate Semialdehyde Decarboxylase


Mass: 14562.349 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Strain: FG41 / Plasmid: pET-3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
References: UniProt: F2Z288, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1173 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 277 K / Method: sitting drop / pH: 7.5
Details: 3 micro liter of protein solution (20.5 mg/mL in 10 mM sodium phosphate buffer, pH 8) mixed with 3 micro liter crystallization solution (0.1 M HEPES-Na buffer, pH 7.5, 2% v/v polyethylene ...Details: 3 micro liter of protein solution (20.5 mg/mL in 10 mM sodium phosphate buffer, pH 8) mixed with 3 micro liter crystallization solution (0.1 M HEPES-Na buffer, pH 7.5, 2% v/v polyethylene glycol 400, 2.0 M ammonium sulfate), Sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 22, 2007
RadiationMonochromator: BLUE MAX-FLUX OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 96503 / Num. obs: 91098 / % possible obs: 85.8 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 2 / Rsym value: 0.154

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CaspRmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AAL

2aal


Resolution: 2.02→40.826 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 4560 5.01 %Random
Rwork0.1936 ---
obs0.196 91098 85.81 %-
all-95653 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→40.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11805 0 70 1173 13048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412111
X-RAY DIFFRACTIONf_angle_d0.76416539
X-RAY DIFFRACTIONf_dihedral_angle_d12.7424235
X-RAY DIFFRACTIONf_chiral_restr0.0431966
X-RAY DIFFRACTIONf_plane_restr0.0032160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0199-2.04290.31540.24932724X-RAY DIFFRACTION83
2.0429-2.06690.33081680.23983052X-RAY DIFFRACTION91
2.0669-2.09210.28111640.23312984X-RAY DIFFRACTION91
2.0921-2.11860.29731510.23623023X-RAY DIFFRACTION90
2.1186-2.14640.27511360.232985X-RAY DIFFRACTION90
2.1464-2.17590.33151700.22582947X-RAY DIFFRACTION89
2.1759-2.20690.31091500.22932922X-RAY DIFFRACTION88
2.2069-2.23990.28551450.21672944X-RAY DIFFRACTION88
2.2399-2.27490.30451400.21112852X-RAY DIFFRACTION86
2.2749-2.31220.25851490.19792854X-RAY DIFFRACTION86
2.3122-2.3520.27381320.20462870X-RAY DIFFRACTION85
2.352-2.39480.24831280.20052801X-RAY DIFFRACTION84
2.3948-2.44090.27571670.19522756X-RAY DIFFRACTION83
2.4409-2.49070.25231480.19172747X-RAY DIFFRACTION82
2.4907-2.54480.25281490.18912736X-RAY DIFFRACTION82
2.5448-2.6040.26791450.19232709X-RAY DIFFRACTION81
2.604-2.66910.2471460.19642687X-RAY DIFFRACTION81
2.6691-2.74130.27231330.20652680X-RAY DIFFRACTION80
2.7413-2.82190.26421340.20142638X-RAY DIFFRACTION78
2.8219-2.9130.24151400.19752613X-RAY DIFFRACTION78
2.913-3.01710.23991530.19442575X-RAY DIFFRACTION77
3.0171-3.13780.24251390.20062594X-RAY DIFFRACTION77
3.1378-3.28060.21931370.19732596X-RAY DIFFRACTION77
3.2806-3.45340.26921330.19142642X-RAY DIFFRACTION78
3.4534-3.66970.21961340.17812769X-RAY DIFFRACTION81
3.6697-3.95280.19831640.16553039X-RAY DIFFRACTION90
3.9528-4.35020.16991810.14453341X-RAY DIFFRACTION98
4.3502-4.97870.15991880.14623425X-RAY DIFFRACTION100
4.9787-6.2690.23481910.19363449X-RAY DIFFRACTION100
6.269-40.83410.25221910.2363584X-RAY DIFFRACTION99

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