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- PDB-2z7b: Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridin... -

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Basic information

Entry
Database: PDB / ID: 2z7b
TitleCrystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase
ComponentsMlr6791 protein
KeywordsLYASE / Class II aldolase superfamily
Function / homology
Function and homology information


3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase / 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase activity / vitamin B6 catabolic process / manganese ion binding
Similarity search - Function
L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMcCulloch, K.M. / Mukherjee, T. / Ealick, S.E. / Begley, T.P.
CitationJournal: Biochemistry / Year: 2007
Title: Gene Identification and Structural Characterization of the Pyridoxal 5'-Phosphate Degradative Protein 3-Hydroxy-2-methylpyridine-4,5-dicarboxylate Decarboxylase from Mesorhizobium loti MAFF303099
Authors: Mukherjee, T. / McCulloch, K.M. / Ealick, S.E. / Begley, T.P.
History
DepositionAug 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Mlr6791 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2732
Polymers30,2181
Non-polymers551
Water3,693205
1
A: Mlr6791 protein
hetero molecules

A: Mlr6791 protein
hetero molecules

A: Mlr6791 protein
hetero molecules

A: Mlr6791 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0948
Polymers120,8744
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.960, 71.960, 90.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Mlr6791 protein / 3-hydroxy-2-methylpyridine-4 / 5-dicarboxylate decarboxylase


Mass: 30218.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: 5335 / Plasmid: pMl5335.XF1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q988D0, 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 1.94 Å3/Da / Density % sol: 36.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 6-9% PEG 8000, 100mM Tris, pH 7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 17813 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.056 / Χ2: 1.293 / Net I/σ(I): 16.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.148 / Num. unique all: 2646 / Χ2: 0.781 / % possible all: 75.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→30.3 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 906 5 %RANDOM
Rwork0.196 ---
obs0.196 17810 98.1 %-
all-17810 --
Solvent computationBsol: 60.057 Å2
Displacement parametersBiso mean: 30.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.098 Å20 Å20 Å2
2--0.098 Å20 Å2
3----0.197 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 1 205 2058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.076
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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