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- PDB-1ps6: Crystal structure of E.coli PdxA -

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Basic information

Entry
Database: PDB / ID: 1ps6
TitleCrystal structure of E.coli PdxA
Components4-hydroxythreonine-4-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / PdxA / 4-hydroxythreonine-4-phosphate dehydrogenase / pyridoxal 5'-phosphate biosynthesis / PLP
Function / homology
Function and homology information


4-hydroxythreonine-4-phosphate dehydrogenase / 4-hydroxythreonine-4-phosphate dehydrogenase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / cobalt ion binding / NAD binding / magnesium ion binding / protein homodimerization activity / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
4-hydroxythreonine-4-phosphate dehydrogenase / PdxA family / Pyridoxal phosphate biosynthetic protein PdxA / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE / 4-hydroxythreonine-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSivaraman, J. / Li, Y. / Banks, J. / Cane, D.E. / Matte, A. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Escherichia coli PdxA, an Enzyme Involved in the Pyridoxal Phosphate Biosynthesis Pathway
Authors: Sivaraman, J. / Li, Y. / Banks, J. / Cane, D.E. / Matte, A. / Cygler, M.
History
DepositionJun 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxythreonine-4-phosphate dehydrogenase
B: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3835
Polymers70,0372
Non-polymers3463
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-97 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.722, 79.141, 114.069
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 / E.C.1.1.1.262 / PdxA / 4-(phosphohydroxy)-L-threonine dehydrogenase / pyridoxal phosphate biosynthetic protein pdxA


Mass: 35018.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PDXA or B0052 / Production host: Escherichia coli (E. coli) / Strain (production host): plasmid
References: UniProt: P19624, 4-hydroxythreonine-4-phosphate dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4TP / 4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE


Mass: 215.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10NO7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.44 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris HCL, PEG 8000, NaOAc, MgCl2, NaKPO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18.1 mg/mlprotein1drop
220 mMTris-HCl1dropp8.
30.2 M1dropNaCl
410 mMdithiothreitol1drop
55 %(w/v)glycerol1drop
67.5 %(w/v)PEG80001reservoir
70.1 M1reservoirpH5.5NaOAc
810 mM1reservoirMgCl2
910 mM1reservoirpH5.9NaKPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 4, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 29956 / Num. obs: 29956 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Rsym value: 0.121 / Net I/σ(I): 9.4
Reflection shellResolution: 2.25→2.33 Å / % possible all: 54.5
Reflection
*PLUS
Num. obs: 29976 / Num. measured all: 157588 / Rmerge(I) obs: 0.121

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Processing

Software
NameClassification
Adxvdata processing
HKL-2000data reduction
SOLVEphasing
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native PdxA

Resolution: 2.25→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2087 -RANDOM
Rwork0.206 ---
all-29956 --
obs-29956 90.3 %-
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4804 0 15 188 5007
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4

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