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- PDB-3mjz: The crystal structure of native FG41 MSAD -

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Basic information

Entry
Database: PDB / ID: 3mjz
TitleThe crystal structure of native FG41 MSAD
ComponentsFG41 Malonate Semialdehyde Decarboxylase
KeywordsISOMERASE / The tautomerase superfamily / Malonate Semialdehyde Decarboxylase / Beta-alpha-beta-motif
Function / homologyTautomerase, MSAD family / Tautomerase enzyme / Lyases; Carbon-carbon lyases; Carboxy-lyases / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / FG41 Malonate Semialdehyde Decarboxylase
Function and homology information
Biological speciesCoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGuo, Y. / Serrano, H. / Poelarends, G.J. / Johnson, W.H.Jr. / 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
DepositionApr 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jan 1, 2014Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)174,74812
Polymers174,74812
Non-polymers00
Water17,925995
1
A: FG41 Malonate Semialdehyde Decarboxylase
B: FG41 Malonate Semialdehyde Decarboxylase
C: FG41 Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)43,6873
Polymers43,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-40 kcal/mol
Surface area14050 Å2
MethodPISA
2
D: FG41 Malonate Semialdehyde Decarboxylase
E: FG41 Malonate Semialdehyde Decarboxylase
F: FG41 Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)43,6873
Polymers43,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-42 kcal/mol
Surface area14100 Å2
MethodPISA
3
G: FG41 Malonate Semialdehyde Decarboxylase
H: FG41 Malonate Semialdehyde Decarboxylase
I: FG41 Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)43,6873
Polymers43,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-44 kcal/mol
Surface area14270 Å2
MethodPISA
4
J: FG41 Malonate Semialdehyde Decarboxylase
K: FG41 Malonate Semialdehyde Decarboxylase
L: FG41 Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)43,6873
Polymers43,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-42 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.955, 94.692, 190.701
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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*PLUS, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 995 / 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 8.0) 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 8.0) 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: 2.02→42.02 Å / Num. obs: 54052 / % possible obs: 85.7 % / Redundancy: 9 % / Rmerge(I) obs: 0.154 / Χ2: 1.937 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.02-2.0990.67390931.618186.7
2.09-2.189.20.56394481.618189.5
2.18-2.279.20.46891771.714187.2
2.27-2.399.30.38989441.73184.8
2.39-2.549.30.32487421.811182.5
2.54-2.749.20.25784971.881180.6
2.74-3.029.10.19982741.957177.8
3.02-3.458.70.12382732.107177.4
3.45-4.357.60.07596412.329189.7
4.35-509.60.063111252.521199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AAL

2aal


Resolution: 2.4→42.02 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.996 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2763 5.1 %RANDOM
Rwork0.2 ---
obs0.204 54052 84.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.97 Å2 / Biso mean: 16.043 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--0.55 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11998 0 0 995 12993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212248
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.94216690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9251558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60823.025562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.526151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.10415118
X-RAY DIFFRACTIONr_chiral_restr0.0930.21966
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029394
X-RAY DIFFRACTIONr_nbd_refined0.2090.25749
X-RAY DIFFRACTIONr_nbtor_refined0.3050.28323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2963
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.219
X-RAY DIFFRACTIONr_mcbond_it0.6161.58018
X-RAY DIFFRACTIONr_mcangle_it1.065212672
X-RAY DIFFRACTIONr_scbond_it1.83234616
X-RAY DIFFRACTIONr_scangle_it2.9874.54018
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 217 -
Rwork0.233 3628 -
all-3845 -
obs--83.03 %

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