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- PDB-4lho: Crystal Structure of FG41Malonate Semialdehyde Decarboxylase inhi... -

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Basic information

Entry
Database: PDB / ID: 4lho
TitleCrystal Structure of FG41Malonate Semialdehyde Decarboxylase inhibited by 3-bromopropiolate
ComponentsFG41 Malonate Semialdehyde Decarboxylase
KeywordsISOMERASE/ISOMERASE INHIBITOR / The tautomerase Superfamily / beta-alpha-beta-motif / Malonate Semialdehyde Decarboxylase / ISOMERASE-ISOMERASE INHIBITOR complex
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 / 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
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 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)74,84925
Polymers72,8125
Non-polymers2,03720
Water6,431357
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)44,90915
Polymers43,6873
Non-polymers1,22212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-102 kcal/mol
Surface area13280 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)44,90915
Polymers43,6873
Non-polymers1,22212
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 area10740 Å2
ΔGint-108 kcal/mol
Surface area13370 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)44,90915
Polymers43,6873
Non-polymers1,22212
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 area10570 Å2
ΔGint-106 kcal/mol
Surface area12850 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-363-

HOH

21E-352-

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, 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
Details: 3-oxopropanoate adduct was a result of reaction of FG41MSAD and its inhibitor bromopropiolate
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: vapor diffusion, hanging drop / pH: 8.5
Details: The best crystals for inactivated FG41 MSAD were obtained at 4C from 6-micro liter hanging drops consisting of equal amounts of precipitant solution [0.1 M TRIS buffer, pH 8.5, 2.0 M (NH4) ...Details: The best crystals for inactivated FG41 MSAD were obtained at 4C from 6-micro liter hanging drops consisting of equal amounts of precipitant solution [0.1 M TRIS buffer, pH 8.5, 2.0 M (NH4)H2PO4] and protein solution (24.5 mg/mL in 10 mM sodium phosphate buffer, pH 8)., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / 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. all: 18824 / % possible obs: 96.4 % / Observed criterion σ(F): 1.33 / Observed criterion σ(I): 2 / Rsym value: 0.116

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Processing

Software
NameVersionClassification
MAR345dtbdata 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: The ligand-free FG41 MSAD was used as the search model for molecular replacement.

Resolution: 2.224→45.609 Å / SU ML: 0.28 / σ(F): 1.33 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 4644 5.06 %Random
Rwork0.164 ---
obs0.166 91715 96.36 %-
all-96301 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.224→45.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 105 357 5382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125122
X-RAY DIFFRACTIONf_angle_d1.2957003
X-RAY DIFFRACTIONf_dihedral_angle_d14.2511781
X-RAY DIFFRACTIONf_chiral_restr0.068821
X-RAY DIFFRACTIONf_plane_restr0.007904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2244-2.24970.37981090.37551450X-RAY DIFFRACTION50
2.2497-2.27620.3558820.32182034X-RAY DIFFRACTION67
2.2762-2.30390.31071230.28522511X-RAY DIFFRACTION82
2.3039-2.33310.30691540.2792834X-RAY DIFFRACTION95
2.3331-2.36380.32232130.23382936X-RAY DIFFRACTION98
2.3638-2.39620.29541670.22562993X-RAY DIFFRACTION100
2.3962-2.43040.2391470.20783027X-RAY DIFFRACTION100
2.4304-2.46670.26421360.19983036X-RAY DIFFRACTION100
2.4667-2.50520.25341410.18812989X-RAY DIFFRACTION100
2.5052-2.54630.21441650.16473069X-RAY DIFFRACTION100
2.5463-2.59020.19251740.16452956X-RAY DIFFRACTION100
2.5902-2.63730.22831600.16192997X-RAY DIFFRACTION100
2.6373-2.6880.20261600.15443048X-RAY DIFFRACTION100
2.688-2.74280.2321560.16613022X-RAY DIFFRACTION100
2.7428-2.80250.20071480.16123011X-RAY DIFFRACTION100
2.8025-2.86770.21851310.16783022X-RAY DIFFRACTION100
2.8677-2.93940.18731630.16733032X-RAY DIFFRACTION100
2.9394-3.01880.20821380.1623022X-RAY DIFFRACTION100
3.0188-3.10760.23161710.16533000X-RAY DIFFRACTION100
3.1076-3.20790.19271650.16482999X-RAY DIFFRACTION100
3.2079-3.32250.24591580.17963024X-RAY DIFFRACTION100
3.3225-3.45550.21181610.17732989X-RAY DIFFRACTION100
3.4555-3.61270.21811910.15863011X-RAY DIFFRACTION100
3.6127-3.80310.20291410.15253019X-RAY DIFFRACTION100
3.8031-4.04120.191900.1422990X-RAY DIFFRACTION100
4.0412-4.3530.1591500.12233027X-RAY DIFFRACTION100
4.353-4.79070.15181440.11923005X-RAY DIFFRACTION100
4.7907-5.48290.19271620.143023X-RAY DIFFRACTION100
5.4829-6.9040.19011420.18143035X-RAY DIFFRACTION100
6.904-45.61820.1582020.17112960X-RAY DIFFRACTION99

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