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- PDB-1vpd: X-Ray Crystal Structure of Tartronate Semialdehyde Reductase [Sal... -

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Basic information

Entry
Database: PDB / ID: 1vpd
TitleX-Ray Crystal Structure of Tartronate Semialdehyde Reductase [Salmonella Typhimurium LT2]
ComponentsTARTRONATE SEMIALDEHYDE REDUCTASE
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / MCSG / PROTEIN STRUCTURE INITIATIVE / REDUCTASE / TARTRONATE / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


2-hydroxy-3-oxopropionate reductase / 2-hydroxy-3-oxopropionate reductase activity / galactarate catabolic process / glyoxylate metabolic process / NAD binding / NADP binding
Similarity search - Function
2-hydroxy-3-oxopropionate reductase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...2-hydroxy-3-oxopropionate reductase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / 2-hydroxy-3-oxopropionate reductase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsOsipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J Struct Funct Genomics / Year: 2009
Title: X-ray crystal structure of GarR-tartronate semialdehyde reductase from Salmonella typhimurium.
Authors: Osipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionOct 22, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionOct 26, 2004ID: 1TEA
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TARTRONATE SEMIALDEHYDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9233
Polymers31,7371
Non-polymers1862
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.275, 105.428, 155.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-542-

HOH

31A-612-

HOH

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Components

#1: Protein TARTRONATE SEMIALDEHYDE REDUCTASE


Mass: 31737.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: GARR / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZLV8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97957
DetectorType: SBC-3 / Detector: CCD / Date: Apr 1, 2004
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 48128 / % possible obs: 87.2 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 34.6
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.75 / % possible all: 44.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.65→40 Å / Cor.coef. Fo:Fc: 0.978 / SU B: 0.873 / SU ML: 0.028 / σ(F): 0 / ESU R: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.144 1979 -RANDOM
Rwork0.12 ---
obs0.121 48124 87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 11 497 2734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222261
X-RAY DIFFRACTIONr_bond_other_d0.0020.022186
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9913057
X-RAY DIFFRACTIONr_angle_other_deg0.84135116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022459
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02374
X-RAY DIFFRACTIONr_nbd_refined0.2240.2520
X-RAY DIFFRACTIONr_nbd_other0.2450.22438
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.21303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8971.51477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50522382
X-RAY DIFFRACTIONr_scbond_it2.5063784
X-RAY DIFFRACTIONr_scangle_it4.0294.5675
X-RAY DIFFRACTIONr_rigid_bond_restr1.28722261
X-RAY DIFFRACTIONr_sphericity_free3.1482498
X-RAY DIFFRACTIONr_sphericity_bonded1.88422236
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 86 -
Rwork0.22 1778 -
obs--4.8 %

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