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- PDB-1jct: Glucarate Dehydratase, N341L mutant Orthorhombic Form -

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Basic information

Entry
Database: PDB / ID: 1jct
TitleGlucarate Dehydratase, N341L mutant Orthorhombic Form
ComponentsGlucarate Dehydratase
KeywordsLYASE / 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
D-GLUCARATE / ISOPROPYL ALCOHOL / Glucarate dehydratase / Glucarate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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: Evolution of Enzymatic Active Sites 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 11, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4May 30, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.5Oct 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_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9778
Polymers98,3922
Non-polymers5856
Water1,72996
1
A: Glucarate Dehydratase
hetero molecules

A: Glucarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9778
Polymers98,3922
Non-polymers5856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4180 Å2
ΔGint-36 kcal/mol
Surface area30490 Å2
MethodPISA
2
B: Glucarate Dehydratase
hetero molecules

B: Glucarate Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9778
Polymers98,3922
Non-polymers5856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4180 Å2
ΔGint-39 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.924, 203.159, 136.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Glucarate Dehydratase /


Mass: 49195.910 Da / Num. of mol.: 2 / Mutation: N341L
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): BL21(DE3)
References: UniProt: P76637, UniProt: P0AES2*PLUS, glucarate dehydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GKR / D-GLUCARATE


Mass: 208.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O8
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Peg5000 monomethylether, 50 mM MgCl, 5% isopropanol, 50 mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl11pH8.0
25 mM11MgCl2
314.5 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-BM
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 23, 2000
RadiationMonochromator: 0.1 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 27057 / Num. obs: 24649 / % possible obs: 91.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.5
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.394 / % possible all: 93.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 100153
Reflection shell
*PLUS
% possible obs: 93.5 %

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Processing

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

1ec8


Resolution: 2.75→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 1182 random
Rwork0.213 --
all-27057 -
obs-24649 -
Displacement parametersBiso mean: 55 Å2
Baniso -1Baniso -2Baniso -3
1-13.5 Å27.7 Å2-21.3 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6801 0 30 104 6935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.449 192 -
Rwork0.347 --
obs-2915 92.3 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor Rfree: 0.449 / Rfactor Rwork: 0.347

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