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- PDB-3pwg: Crystal structure of the mutant S29G.P34A of D-Glucarate dehydrat... -

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Basic information

Entry
Database: PDB / ID: 3pwg
TitleCrystal structure of the mutant S29G.P34A of D-Glucarate dehydratase from Escherichia coli complexed with product 5-keto-4-deoxy-D-Glucarate
ComponentsGlucarate dehydratase
KeywordsLYASE / Enolase superfamily fold / D-Glucarate dehydratase / 5-keto-4-deoxy-D-Glucarate
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 / : / Glucarate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Lukk, T. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the mutant S29G.P34A of D-Glucarate dehydratase from Escherichia Coli complexed with product 5-keto-4-deoxy-D-Glucarate
Authors: Fedorov, A.A. / Fedorov, E.V. / Lukk, T. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 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_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_asym_id / _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_asym_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_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

Downloads & links

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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)197,69715
Polymers196,5634
Non-polymers1,13411
Water3,027168
1
A: Glucarate dehydratase
C: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8037
Polymers98,2822
Non-polymers5215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-38 kcal/mol
Surface area30660 Å2
MethodPISA
2
B: Glucarate dehydratase
D: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8958
Polymers98,2822
Non-polymers6136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-39 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.124, 130.658, 158.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glucarate dehydratase


Mass: 49140.793 Da / Num. of mol.: 4 / Mutation: S29G.P34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 str. EC4042 / Gene: ECH74042_A2717 / Production host: Escherichia coli (E. coli) / References: UniProt: E2KTD9, UniProt: P0AES2*PLUS
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 52.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 0.1M Hepes, 0.2M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→39.874 Å / Num. all: 128604 / Num. obs: 128604 / % possible obs: 92.73 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.874 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 37.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 6462 5.02 %RANDOM
Rwork0.231 ---
all0.2335 128604 --
obs0.2335 128604 92.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.873 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.7359 Å2-0 Å20 Å2
2---6.0884 Å20 Å2
3---20.8242 Å2
Refinement stepCycle: LAST / Resolution: 2→39.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13505 0 74 168 13747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813876
X-RAY DIFFRACTIONf_angle_d1.04818800
X-RAY DIFFRACTIONf_dihedral_angle_d17.4995061
X-RAY DIFFRACTIONf_chiral_restr0.0722049
X-RAY DIFFRACTIONf_plane_restr0.0052459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.4789700.51421292X-RAY DIFFRACTION30
2.0227-2.04650.4994870.48811860X-RAY DIFFRACTION43
2.0465-2.07150.49681470.46042901X-RAY DIFFRACTION66
2.0715-2.09770.46521990.44213633X-RAY DIFFRACTION84
2.0977-2.12530.44941850.41793649X-RAY DIFFRACTION84
2.1253-2.15440.44332130.4064016X-RAY DIFFRACTION92
2.1544-2.18520.40552290.38334078X-RAY DIFFRACTION94
2.1852-2.21780.40242240.37814178X-RAY DIFFRACTION96
2.2178-2.25250.42022300.35134241X-RAY DIFFRACTION97
2.2525-2.28940.4042250.34124233X-RAY DIFFRACTION98
2.2894-2.32890.37772490.32594276X-RAY DIFFRACTION98
2.3289-2.37120.3642170.29954326X-RAY DIFFRACTION99
2.3712-2.41680.33912170.28364354X-RAY DIFFRACTION99
2.4168-2.46610.34421970.27764369X-RAY DIFFRACTION100
2.4661-2.51980.32662230.27074365X-RAY DIFFRACTION100
2.5198-2.57840.32562230.25854352X-RAY DIFFRACTION100
2.5784-2.64280.3222090.26314414X-RAY DIFFRACTION100
2.6428-2.71430.32642340.26044369X-RAY DIFFRACTION100
2.7143-2.79410.29772500.26134346X-RAY DIFFRACTION100
2.7941-2.88430.3382160.26534414X-RAY DIFFRACTION100
2.8843-2.98730.35392600.27074348X-RAY DIFFRACTION100
2.9873-3.10690.3352410.26264398X-RAY DIFFRACTION100
3.1069-3.24820.29662420.24974386X-RAY DIFFRACTION100
3.2482-3.41940.30642340.23174420X-RAY DIFFRACTION100
3.4194-3.63350.26272410.21334387X-RAY DIFFRACTION100
3.6335-3.91380.21492420.18934426X-RAY DIFFRACTION100
3.9138-4.30730.20652410.15974441X-RAY DIFFRACTION100
4.3073-4.92960.19212450.14964456X-RAY DIFFRACTION100
4.9296-6.20690.20222160.16334553X-RAY DIFFRACTION100
6.2069-39.88150.20622560.16334661X-RAY DIFFRACTION100

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