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- PDB-1dxf: 2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli in c... -

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Basic information

Entry
Database: PDB / ID: 1dxf
Title2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli in complex with pyruvate
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 / D-glucarate catabolic process / carbon-carbon lyase 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 family / 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
PYRUVIC ACID / 5-keto-4-deoxy-D-glucarate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 5, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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)55,2346
Polymers55,0102
Non-polymers2254
Water4,396244
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)165,70318
Polymers165,0296
Non-polymers67412
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 area24650 Å2
ΔGint-185.7 kcal/mol
Surface area58520 Å2
MethodPQS
Unit cell
Length a, b, c (Å)126.400, 126.400, 172.000
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: (0.9978, 0.0665, -0.0017), (0.0665, -0.9978, 0.0012), (-0.0016, -0.0013, -1)
Vector: -2.2863, 68.6841, 21.1827)
DetailsBIOLOGICAL_UNIT: HEXAMER

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Components

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


Mass: 27504.865 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-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#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.: 244 / 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: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 232660 / % possible obs: 93.4 % / Redundancy: 14.4 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 14.2
Reflection
*PLUS
Num. obs: 16162 / Num. measured all: 232660
Reflection shell
*PLUS
% possible obs: 72.7 % / Rmerge(I) obs: 0.167

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 754 4.9 %RANDOM
Rwork0.173 ---
obs0.173 15344 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9921 Å2 / ksol: 0.36617 e/Å3
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å23.78 Å20 Å2
2---3.19 Å20 Å2
3---6.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 14 244 4080
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.311.5
X-RAY DIFFRACTIONc_mcangle_it5.132
X-RAY DIFFRACTIONc_scbond_it4.942
X-RAY DIFFRACTIONc_scangle_it6.952.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 98 4.7 %
Rwork0.24 1984 -
obs--76.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4PYR.PAR
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_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor obs: 0.24

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