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- PDB-1jdf: Glucarate Dehydratase from E.coli N341D mutant -

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Basic information

Entry
Database: PDB / ID: 1jdf
TitleGlucarate Dehydratase from E.coli N341D mutant
ComponentsGlucarate Dehydratase
KeywordsLYASE / TIM Barrel / alpha/beta 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, 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
2,3-DIHYDROXY-5-OXO-HEXANEDIOATE / ISOPROPYL ALCOHOL / Glucarate dehydratase / Glucarate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsGulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I.
Citation
Journal: Biochemistry / Year: 2001
Title: Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli.
Authors: Gulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I.
#1: Journal: Biochemistry / Year: 2000
Title: 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.
History
DepositionJun 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)198,13020
Polymers196,7914
Non-polymers1,33816
Water20,4651136
1
A: Glucarate Dehydratase
B: Glucarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,06510
Polymers98,3962
Non-polymers6698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glucarate Dehydratase
D: Glucarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,06510
Polymers98,3962
Non-polymers6698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.925, 83.926, 98.222
Angle α, β, γ (deg.)104.11, 93.75, 113.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glucarate Dehydratase


Mass: 49197.840 Da / Num. of mol.: 4 / Mutation: N341D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P76637, UniProt: P0AES2*PLUS, glucarate dehydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GLR / 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE


Mass: 190.108 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O7
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1136 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8
Details: 14 % MePEG 5000, 50 mM MgCl2, 5 % 2-propanol, 50 mM HEPPS, pH 8.0, microbatch, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMTris-HCl11
25 mM11MgCl2
313.3 mg/mlprotein11
414 %mPEG500012
550 mM12MgCl2
65 %2-propanol12pH8.0
75 %HEPPS12

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 136857 / Num. obs: 132888 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.455 / % possible all: 93.7
Reflection
*PLUS
Num. measured all: 505535
Reflection shell
*PLUS
% possible obs: 89 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1EC8

1ec8


Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.233 6561 Random
Rwork0.198 --
all0.198 136857 -
obs0.198 132888 -
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.37 Å24.2 Å22.17 Å2
2--2.5 Å2-0.15 Å2
3---8.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13644 0 56 1168 14868
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.333 981 -
Rwork0.306 --
obs-19904 93.7 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.333 / Rfactor Rwork: 0.306

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