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- PDB-3mlc: Crystal structure of FG41MSAD inactivated by 3-chloropropiolate -

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Basic information

Entry
Database: PDB / ID: 3mlc
TitleCrystal structure of FG41MSAD inactivated by 3-chloropropiolate
ComponentsFG41 Malonate Semialdehyde Decarboxylase
KeywordsISOMERASE / Tautomerase superfamily / Malonate Semialdehyde Decarboxylase / Beta-alpha-beta-motif / Coryneform bacterium FG41
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
3-chloro-3-oxopropanoic acid / FG41 Malonate Semialdehyde Decarboxylase
Similarity search - Component
Biological speciesCoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.224 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
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Dec 18, 2013Group: Database references
Revision 1.4Oct 8, 2014Group: Structure summary
Revision 1.5Nov 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 1.6Sep 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,42410
Polymers72,8125
Non-polymers6135
Water8,755486
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)44,0556
Polymers43,6873
Non-polymers3683
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-43 kcal/mol
Surface area13830 Å2
MethodPISA
2
D: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules

D: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules

D: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0556
Polymers43,6873
Non-polymers3683
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Buried area8400 Å2
ΔGint-46 kcal/mol
Surface area13660 Å2
MethodPISA
3
E: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules

E: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules

E: FG41 Malonate Semialdehyde Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0556
Polymers43,6873
Non-polymers3683
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area8310 Å2
ΔGint-42 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.227, 144.227, 144.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11D-183-

HOH

21E-403-

HOH

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Components

#1: Protein
FG41 Malonate Semialdehyde Decarboxylase


Mass: 14562.349 Da / Num. of mol.: 5
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: Chemical
ChemComp-PR6 / 3-chloro-3-oxopropanoic acid


Mass: 122.507 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H3ClO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 277 K / Method: sitting drop / pH: 8.5
Details: 3 micro liter of protein solution (24.5 mg/mL in 10 mM sodium phosphate buffer, pH 8) mixed with 3 micro liter crystallization solution (0.1 M Tris hydrochloride buffer, pH 8.5, 2.0 M mono- ...Details: 3 micro liter of protein solution (24.5 mg/mL in 10 mM sodium phosphate buffer, pH 8) mixed with 3 micro liter crystallization solution (0.1 M Tris hydrochloride buffer, pH 8.5, 2.0 M mono-ammonium dihydrogen phosphate), Sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 25, 2007
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→102.06 Å / Num. obs: 47735 / % possible obs: 95.1 % / Redundancy: 33.1 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.1
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 2 % / Rmerge(I) obs: 0.894 / % possible all: 55.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MJZ

3mjz


Resolution: 2.224→102.06 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.372 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27504 2398 5 %RANDOM
Rwork0.22394 ---
obs0.2265 45095 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.467 Å2
Refinement stepCycle: LAST / Resolution: 2.224→102.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 0 30 486 5427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225036
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9496856
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43823230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98315763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6431548
X-RAY DIFFRACTIONr_chiral_restr0.1270.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023873
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.22403
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23360
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2501
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.2143
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.53299
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21725185
X-RAY DIFFRACTIONr_scbond_it2.15831907
X-RAY DIFFRACTIONr_scangle_it3.2584.51671
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.224→2.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 110 -
Rwork0.384 2076 -
obs--60.98 %

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