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- PDB-3flk: Crystal Structure of Tartrate Dehydrogenase from Pseudomonas puti... -

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Basic information

Entry
Database: PDB / ID: 3flk
TitleCrystal Structure of Tartrate Dehydrogenase from Pseudomonas putida in complex with NADH, oxalate and metal ion
ComponentsTartrate dehydrogenase/decarboxylase
KeywordsOXIDOREDUCTASE / Lyase / Magnesium / Manganese / NAD
Function / homology
Function and homology information


D-malate dehydrogenase (decarboxylating) / tartrate dehydrogenase / tartrate decarboxylase / tartrate dehydrogenase activity / D-malate dehydrogenase (decarboxylating) (NAD+) activity / tartrate decarboxylase activity / NAD binding / magnesium ion binding / cytoplasm
Similarity search - Function
Tartrate dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / AMMONIUM ION / OXALATE ION / Tartrate dehydrogenase/decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMalik, R. / Viola, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions.
Authors: Malik, R. / Viola, R.E.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Non-polymer description
Revision 1.3Oct 20, 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_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_asym_id / _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_asym_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.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_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: Tartrate dehydrogenase/decarboxylase
B: Tartrate dehydrogenase/decarboxylase
C: Tartrate dehydrogenase/decarboxylase
D: Tartrate dehydrogenase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,12237
Polymers164,1314
Non-polymers4,99133
Water16,556919
1
A: Tartrate dehydrogenase/decarboxylase
B: Tartrate dehydrogenase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,48418
Polymers82,0662
Non-polymers2,41816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-136 kcal/mol
Surface area25370 Å2
MethodPISA
2
C: Tartrate dehydrogenase/decarboxylase
D: Tartrate dehydrogenase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,63819
Polymers82,0662
Non-polymers2,57317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-141 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.278, 117.278, 291.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tartrate dehydrogenase/decarboxylase / TDH / D-malate dehydrogenase


Mass: 41032.758 Da / Num. of mol.: 4 / Mutation: G79D, V243 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: ATCC 17642 / Plasmid: pet-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q51945, tartrate dehydrogenase

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Non-polymers , 7 types, 952 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#5: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.75 M ammonium sulfate, 0.2 M potassium acetate, 0.02 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→109.11 Å / Num. obs: 126431 / % possible obs: 99 % / Redundancy: 12.2 % / Rsym value: 0.112 / Net I/σ(I): 21.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.97 / Rsym value: 0.307 / % possible all: 90

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.441 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22692 6868 5 %RANDOM
Rwork0.20764 ---
obs0.20862 126431 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11248 0 302 919 12469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211813
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.97716064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12451432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82423.768552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.481151864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.481584
X-RAY DIFFRACTIONr_chiral_restr0.0760.21722
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029056
X-RAY DIFFRACTIONr_nbd_refined0.1780.25821
X-RAY DIFFRACTIONr_nbtor_refined0.2990.28011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0860.21010
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.225
X-RAY DIFFRACTIONr_mcbond_it0.4591.57384
X-RAY DIFFRACTIONr_mcangle_it0.681211459
X-RAY DIFFRACTIONr_scbond_it0.97135100
X-RAY DIFFRACTIONr_scangle_it1.4984.54605
LS refinement shellResolution: 2→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 432 -
Rwork0.246 8439 -
obs--88.25 %

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