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- PDB-1bqg: THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOM... -

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Basic information

Entry
Database: PDB / ID: 1bqg
TitleTHE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA
ComponentsD-GLUCARATE DEHYDRATASE
KeywordsGLUCARATE / TIM BARREL / ENOLASE SUPERFAMILY
Function / homology
Function and homology information


glucarate dehydratase activity / D-glucarate catabolic process / glucarate dehydratase / magnesium ion binding
Similarity search - Function
Glucarate dehydratase / D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain ...Glucarate dehydratase / D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucarate dehydratase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsGulick, A.M. / Palmer, D.R.J. / Babbitt, P.C. / Gerlt, J.A. / Rayment, I.
CitationJournal: Biochemistry / Year: 1998
Title: Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.
Authors: Gulick, A.M. / Palmer, D.R. / Babbitt, P.C. / Gerlt, J.A. / Rayment, I.
History
DepositionAug 15, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-GLUCARATE DEHYDRATASE


Theoretical massNumber of molelcules
Total (without water)49,6321
Polymers49,6321
Non-polymers00
Water2,612145
1
A: D-GLUCARATE DEHYDRATASE

A: D-GLUCARATE DEHYDRATASE

A: D-GLUCARATE DEHYDRATASE

A: D-GLUCARATE DEHYDRATASE


Theoretical massNumber of molelcules
Total (without water)198,5284
Polymers198,5284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)69.623, 108.786, 122.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein D-GLUCARATE DEHYDRATASE


Mass: 49632.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / References: UniProt: P42206, glucarate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 7 / Details: pH 7
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.4 mg/mlprotein11
219 %PEG100011
3100 mMsodium formate11
4100 mMBTP11

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 2, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 28914 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.202 / Rsym value: 0.202 / % possible all: 71
Reflection
*PLUS
Num. measured all: 72242
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 70.8 %

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Processing

Software
NameVersionClassification
HEAVYmodel building
TNT5Drefinement
XDSdata reduction
XSCALIBREdata scaling
HEAVYphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.19 --
all0.19 20284 -
obs-20284 96 %
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 0 145 3186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.015
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.089
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.015

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