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- PDB-2hi1: The structure of a putative 4-hydroxythreonine-4-phosphate dehydr... -

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Basic information

Entry
Database: PDB / ID: 2hi1
TitleThe structure of a putative 4-hydroxythreonine-4-phosphate dehydrogenase from Salmonella typhimurium.
Components4-hydroxythreonine-4-phosphate dehydrogenase 2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyridoxal phosphate biosynthesis / Salmonella Typhimurium / 4-hydroxythreonine-4-phosphate dehydrogenase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


4-phospho-D-threonate 3-dehydrogenase / NAD binding / oxidoreductase activity / metal ion binding
Similarity search - Function
PdxA family / Pyridoxal phosphate biosynthetic protein PdxA / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-threonate 4-phosphate dehydrogenase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsCuff, M.E. / Quartey, P. / Holzle, D. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a putative 4-hydroxythreonine-4-phosphate dehydrogenase from Salmonella typhimurium.
Authors: Cuff, M.E. / Quartey, P. / Holzle, D. / Joachimiak, A.
History
DepositionJun 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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
Remark 300Author states that biological unit for the protein is not yet known

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxythreonine-4-phosphate dehydrogenase 2
B: 4-hydroxythreonine-4-phosphate dehydrogenase 2


Theoretical massNumber of molelcules
Total (without water)71,5102
Polymers71,5102
Non-polymers00
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-16 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.660, 92.892, 101.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 4-hydroxythreonine-4-phosphate dehydrogenase 2 / 4-(phosphohydroxy)-L-threonine dehydrogenase 2


Mass: 35754.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: pdxA2 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P58718, 4-hydroxythreonine-4-phosphate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Na formate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918, 0.97932
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979321
ReflectionResolution: 2.3→39.9 Å / Num. all: 28553 / Num. obs: 28553 / % possible obs: 90.59 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.198 / Rsym value: 0.411 / % possible all: 64.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
autoSHARPphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.3→39.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.915 / SU B: 15.301 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.386 / ESU R Free: 0.278
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26613 1559 5.2 %RANDOM
Rwork0.187 ---
all0.191 28553 --
obs0.191 28553 90.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.851 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20 Å2
2--4.51 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 0 422 5283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224983
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9756774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6823.542192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18915832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6481533
X-RAY DIFFRACTIONr_chiral_restr0.10.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023698
X-RAY DIFFRACTIONr_nbd_refined0.2160.22490
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2314
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.210
X-RAY DIFFRACTIONr_mcbond_it0.8081.53317
X-RAY DIFFRACTIONr_mcangle_it1.2225174
X-RAY DIFFRACTIONr_scbond_it1.81931859
X-RAY DIFFRACTIONr_scangle_it2.7884.51599
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 77 -
Rwork0.225 1567 -
obs--67.71 %
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)
11.35170.2763-0.01131.0972-0.29463.11960.08490.00720.0496-0.0378-0.01330.0058-0.2294-0.0855-0.0716-0.2250.0282-0.005-0.17140.0077-0.186311.814781.4239-6.864
20.459-0.141-0.33010.6761-0.56523.58640.02840.0461-0.0850.0696-0.0270.04710.1929-0.4836-0.0014-0.2239-0.0519-0.0079-0.1-0.01-0.17469.034671.357717.5483
32.6248-0.07380.30233.0693-0.8034.12120.0268-0.6673-0.71920.3856-0.01510.2332-0.0019-0.099-0.0117-0.28190.00240.04770.07850.2094-0.082228.650456.397955.1898
42.2924-0.4389-0.04651.2676-1.0272.7343-0.0343-0.1436-0.0861-0.0599-0.01270.0622-0.0080.21310.0471-0.2340.0058-0.0043-0.1692-0.015-0.231828.576370.648633.169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1555 - 158
2X-RAY DIFFRACTION2AA156 - 327159 - 330
3X-RAY DIFFRACTION3BB3 - 1556 - 158
4X-RAY DIFFRACTION4BB156 - 327159 - 330

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