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- PDB-1ps7: Crystal structure of E.coli PdxA -

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Basic information

Entry
Database: PDB / ID: 1ps7
TitleCrystal structure of E.coli PdxA
Components4-hydroxythreonine-4-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / pyridoxine biosynthesis
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-hydroxythreonine-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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 1.4Apr 3, 2024Group: 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_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.conn_type_id / _struct_conn.id / _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
Revision 1.5Nov 20, 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: 4-hydroxythreonine-4-phosphate dehydrogenase
B: 4-hydroxythreonine-4-phosphate dehydrogenase
C: 4-hydroxythreonine-4-phosphate dehydrogenase
D: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,1738
Polymers141,9124
Non-polymers2624
Water8,179454
1
A: 4-hydroxythreonine-4-phosphate dehydrogenase
B: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0874
Polymers70,9562
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-98 kcal/mol
Surface area24370 Å2
MethodPISA
2
C: 4-hydroxythreonine-4-phosphate dehydrogenase
D: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0874
Polymers70,9562
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-97 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.050, 76.693, 95.424
Angle α, β, γ (deg.)90.00, 109.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35477.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PDXA OR B0052 / Plasmid: pF04 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: P19624, 4-hydroxythreonine-4-phosphate dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.26 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Citrate, MgCl2, PEG 8K, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / 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
620 %(w/v)PEG80001reservoir
7100 mMHEPES1reservoirpH7.5
875 mMcitrate1reservoir
9100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.995 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 17, 2002
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 44107 / Num. obs: 44107 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.092 / Net I/σ(I): 9.4
Reflection shellResolution: 2.47→2.54 Å / % possible all: 63.5
Reflection
*PLUS
Num. obs: 44115 / Num. measured all: 232767 / Rmerge(I) obs: 0.092

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Processing

Software
NameClassification
Adxvdata processing
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PdxA native model

Resolution: 2.47→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2204 -RANDOM
Rwork0.213 ---
all-44107 --
obs-44107 95.5 %-
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.47→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9568 0 4 454 10026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.5
Refinement
*PLUS
Highest resolution: 2.45 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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