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- PDB-3pwi: Crystal structure of the mutant P34A of D-Glucarate dehydratase f... -

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Basic information

Entry
Database: PDB / ID: 3pwi
TitleCrystal structure of the mutant 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: 2.2296 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9558
Polymers98,3422
Non-polymers6136
Water2,738152
1
A: Glucarate dehydratase
hetero molecules

A: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9558
Polymers98,3422
Non-polymers6136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3960 Å2
ΔGint-36 kcal/mol
Surface area29800 Å2
MethodPISA
2
B: Glucarate dehydratase
hetero molecules

B: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9558
Polymers98,3422
Non-polymers6136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area4010 Å2
ΔGint-34 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.784, 128.925, 71.419
Angle α, β, γ (deg.)90.00, 96.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

21B-523-

HOH

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Components

#1: Protein Glucarate dehydratase /


Mass: 49170.820 Da / Num. of mol.: 2 / Mutation: 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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GLR / 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE


Mass: 190.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 20% PEG 8000, 0.1M CAPS, 0.2M sodium chloride, pH 10.5, 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: 2.2296→38.865 Å / Num. all: 63952 / Num. obs: 63952 / % possible obs: 96.95 % / 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: 2.2296→38.865 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 3239 5.06 %RANDOM
Rwork0.2048 ---
all0.2071 63952 --
obs0.2071 63952 96.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.142 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3391 Å20 Å23.2455 Å2
2--12.9949 Å2-0 Å2
3----11.6557 Å2
Refinement stepCycle: LAST / Resolution: 2.2296→38.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6817 0 40 152 7009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087005
X-RAY DIFFRACTIONf_angle_d1.0579490
X-RAY DIFFRACTIONf_dihedral_angle_d17.6032560
X-RAY DIFFRACTIONf_chiral_restr0.0721034
X-RAY DIFFRACTIONf_plane_restr0.0051243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2296-2.26290.35831240.31582079X-RAY DIFFRACTION77
2.2629-2.29820.31411300.29662546X-RAY DIFFRACTION94
2.2982-2.33590.34791300.27062593X-RAY DIFFRACTION96
2.3359-2.37620.34821230.25812675X-RAY DIFFRACTION97
2.3762-2.41940.30731390.23642607X-RAY DIFFRACTION97
2.4194-2.46590.28541520.24842633X-RAY DIFFRACTION97
2.4659-2.51620.3151370.2442634X-RAY DIFFRACTION98
2.5162-2.57090.30671390.24082655X-RAY DIFFRACTION98
2.5709-2.63070.30441420.23892693X-RAY DIFFRACTION98
2.6307-2.69650.29871540.24552653X-RAY DIFFRACTION98
2.6965-2.76940.26141270.24512715X-RAY DIFFRACTION98
2.7694-2.85090.31391420.24522669X-RAY DIFFRACTION98
2.8509-2.94290.31441510.24922643X-RAY DIFFRACTION99
2.9429-3.0480.31591390.25262691X-RAY DIFFRACTION99
3.048-3.170.30581370.24222683X-RAY DIFFRACTION98
3.17-3.31420.27051420.23082700X-RAY DIFFRACTION99
3.3142-3.48880.27391590.22182665X-RAY DIFFRACTION99
3.4888-3.70720.24721640.20922677X-RAY DIFFRACTION99
3.7072-3.99320.2261500.1812679X-RAY DIFFRACTION98
3.9932-4.39460.21391450.1652668X-RAY DIFFRACTION98
4.3946-5.02930.17721460.14462697X-RAY DIFFRACTION98
5.0293-6.3320.18811370.15882724X-RAY DIFFRACTION99
6.332-38.8710.18811300.15822734X-RAY DIFFRACTION97

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