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- PDB-1ecq: E. COLI GLUCARATE DEHYDRATASE BOUND TO 4-DEOXYGLUCARATE -

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Basic information

Entry
Database: PDB / ID: 1ecq
TitleE. COLI GLUCARATE DEHYDRATASE BOUND TO 4-DEOXYGLUCARATE
ComponentsGLUCARATE DEHYDRATASE
KeywordsLYASE / Glucarate Dehydratase Enolase Enzyme Superfamily TIM Barrel (beta/alpha)7beta barrel
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, 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 ...Glucarate dehydratase / D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / 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
4-DEOXYGLUCARATE / ISOPROPYL ALCOHOL / Glucarate dehydratase / Glucarate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsGulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I.
Citation
Journal: Biochemistry / Year: 2000
Title: Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli.
Authors: Gulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I.
#1: Journal: Biochemistry / Year: 1998
Title: Evolution of Enzymative 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
DepositionJan 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.4Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCARATE DEHYDRATASE
B: GLUCARATE DEHYDRATASE
C: GLUCARATE DEHYDRATASE
D: GLUCARATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,89416
Polymers196,7874
Non-polymers1,10612
Water16,232901
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.108, 84.602, 98.779
Angle α, β, γ (deg.)103.46, 93.97, 113.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GLUCARATE DEHYDRATASE


Mass: 49196.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET / Production host: Escherichia coli (E. coli)
References: UniProt: P76637, UniProt: P0AES2*PLUS, glucarate dehydratase
#2: Chemical
ChemComp-DXG / 4-DEOXYGLUCARATE


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
Details: NaBH4 reduction of 5-ketodeoxyglucarate, purification by anion exchange
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8
Details: 1:1 mixture of protein and 14 % PEG5000 Monomethylether 75 mM MgCl2 5 % isopropanol 50 mM Hepp, pH 8.0, microbatch, temperature 4.0K
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
Method: batch method / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 %PEG5000 ME11
275 mM11MgCl2
35 %2-propanol11
450 mMHEPPES11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1201
DetectorType: OTHER / Detector: CCD / Date: Jul 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1201 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 511237 / Num. obs: 511021 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 11
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.321 / Num. unique all: 12700 / % possible all: 94.2
Reflection
*PLUS
Num. obs: 131655 / Num. measured all: 511237
Reflection shell
*PLUS
% possible obs: 94.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.305 6432 RANDOM
Rwork0.209 --
all0.209 139366 -
obs0.209 127330 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13670 0 56 917 14643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.01
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / Rfactor all: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.01
X-RAY DIFFRACTIONt_planar_d0.004
X-RAY DIFFRACTIONt_plane_restr0.012

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