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- PDB-1dxe: 2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1dxe
Title2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli
Components2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
KeywordsCLASS II ALDOLASE
Function / homology
Function and homology information


2-dehydro-3-deoxyglucarate aldolase / 2-dehydro-3-deoxyglucarate aldolase activity / glucarate catabolic process / galactarate catabolic process / carbon-carbon lyase activity / D-glucarate catabolic process / 2-dehydro-3-deoxy-D-gluconate aldolase activity / aldehyde-lyase activity / magnesium ion binding / cytoplasm
Similarity search - Function
5-keto-4-deoxy-D-glucarate aldolase / : / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 5-keto-4-deoxy-D-glucarate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsIzard, T. / Blackwell, N.C.
CitationJournal: Embo J. / Year: 2000
Title: Crystal Structures of the Metal-Dependent 2-Dehydro-3-Deoxy-Galactarate Aldolase Suggest a Novel Reaction Mechanism.
Authors: Izard, T. / Blackwell, N.C.
History
DepositionJan 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
B: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2518
Polymers54,8222
Non-polymers4286
Water11,818656
1
A: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
B: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
hetero molecules

A: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
B: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
hetero molecules

A: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
B: 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,75224
Polymers164,4666
Non-polymers1,28518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area25260 Å2
ΔGint-214.9 kcal/mol
Surface area59220 Å2
MethodPQS
Unit cell
Length a, b, c (Å)129.070, 129.070, 167.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.997, 0.0769, -0.0075), (0.0769, -0.997, 0.0038), (-0.0072, -0.0044, -1)
Vector: -2.6666, 69.4699, 23.4231)
DetailsBIOLOGICAL_UNIT: HEXAMER

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Components

#1: Protein 2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE


Mass: 27411.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli)
References: UniProt: P23522, 2-dehydro-3-deoxyglucarate aldolase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 1.34 Å3/Da / Density % sol: 48 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Blackwell, N.C., (1999) Acta Crystallogr., D55, 1368.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMpotassium phosphate1drop
25 mMmagnesium sulfate1drop
37 mg/mlenzyme1drop
44 %PEG30001reservoir
50.2 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8855, 0.9783, 0.9785
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88551
20.97831
30.97851
ReflectionResolution: 1.82→20 Å / Num. obs: 1386204 / % possible obs: 99.7 % / Redundancy: 29.1 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 83.3
Reflection
*PLUS
Num. obs: 47695 / Num. measured all: 1386204
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.336

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2305 5 %RANDOM
Rwork0.171 ---
obs0.171 46201 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1746 Å2 / ksol: 0.352355 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.52 Å20 Å2
2---0.93 Å20 Å2
3---1.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 22 656 4500
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.381.5
X-RAY DIFFRACTIONc_mcangle_it0.652
X-RAY DIFFRACTIONc_scbond_it0.572
X-RAY DIFFRACTIONc_scangle_it0.892.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 255 4.7 %
Rwork0.214 5124 -
obs--65.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.26 / Rfactor obs: 0.214

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