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- PDB-5dt9: Crystal structure of a putative D-Erythronate-4-Phosphate Dehydro... -

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Basic information

Entry
Database: PDB / ID: 5dt9
TitleCrystal structure of a putative D-Erythronate-4-Phosphate Dehydrogenase from Vibrio cholerae
ComponentsErythronate-4-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / CSGID / Center for Structural Genomics of Infectious Diseases / NAD binding / dehydrogenase / erythronate-4-phosphate dehydrogenase
Function / homology
Function and homology information


4-phosphoerythronate dehydrogenase / 4-phosphoerythronate dehydrogenase activity / 'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxine biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / protein dimerization activity / cytosol
Similarity search - Function
Erythronate-4-phosphate dehydrogenase, dimerisation domain / Erythronate-4-phosphate dehydrogenase / Erythronate-4-phosphate dehydrogenase, dimerisation domain / PdxB, dimerisation domain superfamily / Domain of unknown function (DUF3410) / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain ...Erythronate-4-phosphate dehydrogenase, dimerisation domain / Erythronate-4-phosphate dehydrogenase / Erythronate-4-phosphate dehydrogenase, dimerisation domain / PdxB, dimerisation domain superfamily / Domain of unknown function (DUF3410) / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / Ribosomal Protein S8; Chain: A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Erythronate-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.663 Å
AuthorsStogios, P.J. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of a putative D-Erythronate-4-Phosphate Dehydrogenase from Vibrio cholerae
Authors: Stogios, P.J.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythronate-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,27414
Polymers42,5791
Non-polymers1,69513
Water2,774154
1
A: Erythronate-4-phosphate dehydrogenase
hetero molecules

A: Erythronate-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,54828
Polymers85,1582
Non-polymers3,39026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7980 Å2
ΔGint-269 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.775, 145.775, 62.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

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Components

#1: Protein Erythronate-4-phosphate dehydrogenase


Mass: 42578.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: pdxB, VC_2108 / Plasmid: pCPD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9KQ92, 4-phosphoerythronate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M ammonium sulfate, 0.1M Hepes pH 7.5, 2% PEG400, 1 mM Glutamic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.66→25 Å / Num. obs: 18676 / % possible obs: 94.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.39
Reflection shellResolution: 2.66→2.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.462 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphenix.phaserphasing
Cootmodel building
PHENIXphenix.autobuildmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OET

3oet


Resolution: 2.663→25 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 1526 5.05 %Random selection
Rwork0.1929 ---
obs0.1953 17063 91.36 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.663→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 96 154 3177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033084
X-RAY DIFFRACTIONf_angle_d1.3854201
X-RAY DIFFRACTIONf_dihedral_angle_d13.4041126
X-RAY DIFFRACTIONf_chiral_restr0.038477
X-RAY DIFFRACTIONf_plane_restr0.003533
LS refinement shellResolution: 2.6635→2.7494 Å / Rfactor Rfree: 0.3454 / Rfactor Rwork: 0.2765
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8577-0.1396-1.34313.3093-0.19325.5285-0.02470.24790.02450.041-0.10340.2809-0.067-0.06580.12710.3261-0.01560.04190.3109-0.02640.5309-0.722356.9456.3211
22.8140.00870.48942.9459-0.13731.7735-0.1744-0.52610.2480.46580.126-0.2017-0.00520.10680.03910.42650.1537-0.05890.4694-0.05450.493730.140847.489716.7691
32.9887-1.8052-0.51142.07680.48930.5577-0.0945-0.003-0.56430.06170.01740.21820.17210.08920.07120.35880.059-0.0370.38160.02860.481518.947139.09953.0575
43.11140.685-0.56456.4534-1.03734.589-0.2359-0.2665-0.47580.17180.17350.64990.6881-0.45960.09150.47710.12230.12250.54130.06110.626119.222126.8928.7609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:95)
2X-RAY DIFFRACTION2(chain A and resid 96:272)
3X-RAY DIFFRACTION3(chain A and resid 273:350)
4X-RAY DIFFRACTION4(chain A and resid 351:382)

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