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

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Basic information

Entry
Database: PDB / ID: 2aag
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: 1.85 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: Version format compliance
Revision 1.3Mar 29, 2017Group: Refinement description
Revision 1.4Oct 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 1.5Feb 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 1.6Apr 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
C: Malonate Semialdehyde Decarboxylase
D: Malonate Semialdehyde Decarboxylase
E: Malonate Semialdehyde Decarboxylase
F: Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)85,0866
Polymers85,0866
Non-polymers00
Water14,538807
1
A: Malonate Semialdehyde Decarboxylase
B: Malonate Semialdehyde Decarboxylase
C: Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)42,5433
Polymers42,5433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-25 kcal/mol
Surface area14130 Å2
MethodPISA
2
D: Malonate Semialdehyde Decarboxylase
E: Malonate Semialdehyde Decarboxylase
F: Malonate Semialdehyde Decarboxylase


Theoretical massNumber of molelcules
Total (without water)42,5433
Polymers42,5433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-24 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.709, 82.105, 77.603
Angle α, β, γ (deg.)90.00, 101.15, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: 1

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALAA1 - 1291 - 129
2GLYGLYBB1 - 1301 - 130
3VALVALCC1 - 1291 - 129
4VALVALDD1 - 1291 - 129
5VALVALEE1 - 1291 - 129
6VALVALFF1 - 1291 - 129
Detailsthe biological unit is a homotrimer; two of which crystallized in the asymmetric unit.

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Components

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


Mass: 14180.961 Da / Num. of mol.: 6
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.: 807 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 35% (v/v) 1,6-hexanediol, 200 mM MgCl2, and 100 mM Tris-Cl buffer, pH 8.0, 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 6, 2004 / Details: Osmic Blue Max-Flux Confocal optical system
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. all: 63310 / Num. obs: 60986 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Biso Wilson estimate: 22.45 Å2 / Rsym value: 0.072 / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: c-alpha trace of density map resulting from a single-wavelength anomalous difference data set (using Hg's anomalous signal)

Resolution: 1.85→19.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.351 / SU ML: 0.103 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23178 2992 5.1 %RANDOM
Rwork0.17826 ---
all0.1783 60612 --
obs0.181 55695 96.82 %-
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: 23.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-1.58 Å2
2--0.09 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 0 807 6759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0216072
X-RAY DIFFRACTIONr_angle_refined_deg2.3251.9678219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1465771
X-RAY DIFFRACTIONr_chiral_restr0.180.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024635
X-RAY DIFFRACTIONr_nbd_refined0.2220.23003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2726
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.224
X-RAY DIFFRACTIONr_mcbond_it1.0161.53831
X-RAY DIFFRACTIONr_mcangle_it1.71926120
X-RAY DIFFRACTIONr_scbond_it2.62832241
X-RAY DIFFRACTIONr_scangle_it4.2254.52099
X-RAY DIFFRACTIONr_rigid_bond_restr1.79726072
X-RAY DIFFRACTIONr_sphericity_free5.2522807
X-RAY DIFFRACTIONr_sphericity_bonded1.10425963
Refine LS restraints NCS

Ens-ID: 1 / Number: 968 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.140.05
2Btight positional0.190.05
3Ctight positional0.160.05
4Dtight positional0.150.05
5Etight positional0.160.05
6Ftight positional0.150.05
1Atight thermal0.290.5
2Btight thermal0.270.5
3Ctight thermal0.270.5
4Dtight thermal0.280.5
5Etight thermal0.270.5
6Ftight thermal0.280.5
LS refinement shellResolution: 1.85→1.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 40
RfactorNum. reflection
Rfree0.271 119
Rwork0.211 2040
all-2159

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