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- PDB-2aaj: Crystal Structures of the Wild-type, Mutant-P1A and Inactivated M... -

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Basic information

Entry
Database: PDB / ID: 2aaj
TitleCrystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities
ComponentsMalonate Semialdehyde Decarboxylase
KeywordsLYASE / tautomerase superfamily / beta-alpha-beta / homotrimeric
Function / homologyTautomerase, MSAD family / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / Malonate semialdehyde decarboxylase
Function and homology information
Biological speciesPseudomonas pavonaceae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsAlmrud, J.J. / Poelarends, G.J. / Johnson Jr., W.H. / Serrano, H. / Hackert, M.L. / Whitman, C.P.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structures of the Wild-Type, P1A Mutant, and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities
Authors: Almrud, J.J. / Poelarends, G.J. / Johnson Jr., W.H. / Serrano, H. / Hackert, M.L. / Whitman, C.P.
History
DepositionJul 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Apr 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: Malonate Semialdehyde Decarboxylase
B: Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)28,2262
Polymers28,2262
Non-polymers00
Water3,423190
1
A: Malonate Semialdehyde Decarboxylase

A: Malonate Semialdehyde Decarboxylase

A: Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)42,3393
Polymers42,3393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation9_564y,z+1,x-11
Buried area8220 Å2
ΔGint-28 kcal/mol
Surface area14100 Å2
MethodPISA, PQS
2
B: Malonate Semialdehyde Decarboxylase

B: Malonate Semialdehyde Decarboxylase

B: Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)42,3393
Polymers42,3393
Non-polymers00
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 area8260 Å2
ΔGint-25 kcal/mol
Surface area14150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.152, 110.152, 110.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Cell settingcubic
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-181-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 1 - 129 / Label seq-ID: 1 - 129

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a homotrimer. In this crystal form two independent monomers comprise the asymmetric unit. The biological assembly is generated by the crystallographic symmetry operator

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Components

#1: Protein Malonate Semialdehyde Decarboxylase / E.C.4.1.1.-


Mass: 14112.889 Da / Num. of mol.: 2 / Mutation: P1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas pavonaceae (bacteria) / Strain: 170 / Gene: orf130 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9EV83, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.8 M Li(CH3COO), 0.7 M (NH4)2SO4, and 100 mM sodium citrate buffer (pH 5.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.74→29.4 Å / Num. all: 12097 / Num. obs: 11976 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.2
Reflection shellResolution: 2.74→2.86 Å / Rmerge(I) obs: 0.391 / Num. unique all: 1188 / % possible all: 98.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wildtype MSAD

Resolution: 2.74→29.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.306 / SU ML: 0.182 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 623 5.2 %RANDOM
Rwork0.1614 ---
all0.1641 11328 --
obs0.1641 11251 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.56 Å2
Refinement stepCycle: LAST / Resolution: 2.74→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 0 190 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212009
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.9642719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7925256
X-RAY DIFFRACTIONr_chiral_restr0.1220.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021530
X-RAY DIFFRACTIONr_nbd_refined0.2140.2845
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.224
X-RAY DIFFRACTIONr_mcbond_it0.7891.51272
X-RAY DIFFRACTIONr_mcangle_it1.41722030
X-RAY DIFFRACTIONr_scbond_it1.9893737
X-RAY DIFFRACTIONr_scangle_it3.2924.5689
X-RAY DIFFRACTIONr_rigid_bond_restr1.11322009
X-RAY DIFFRACTIONr_sphericity_free3.5992190
X-RAY DIFFRACTIONr_sphericity_bonded1.10521975
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 986 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.090.05
tight thermal0.10.5
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.318 37
Rwork0.246 814
obs-814

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