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- PDB-1m5w: 1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in C... -

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Basic information

Entry
Database: PDB / ID: 1m5w
Title1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate
ComponentsPyridoxal phosphate biosynthetic protein pdxJ
KeywordsBIOSYNTHETIC PROTEIN / TIM barrel / protein-substrate complex / multi-binding states
Function / homology
Function and homology information


pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / identical protein binding / cytosol
Similarity search - Function
Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ / Pyridoxine 5'-phosphate synthase / Pyridoxal phosphate biosynthesis protein PdxJ / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-DEOXY-D-XYLULOSE-5-PHOSPHATE / PHOSPHATE ION / Pyridoxine 5'-phosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsYeh, J.I. / Du, S. / Pohl, E. / Cane, D.E.
CitationJournal: Biochemistry / Year: 2002
Title: Multistate Binding in Pyridoxine 5'-Phosphate Synthase: 1.96 A Crystal Structure in Complex with 1-deoxy-D-xylulose phosphate
Authors: Yeh, J.I. / Du, S. / Pohl, E. / Cane, D.E.
History
DepositionJul 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal phosphate biosynthetic protein pdxJ
B: Pyridoxal phosphate biosynthetic protein pdxJ
C: Pyridoxal phosphate biosynthetic protein pdxJ
D: Pyridoxal phosphate biosynthetic protein pdxJ
E: Pyridoxal phosphate biosynthetic protein pdxJ
F: Pyridoxal phosphate biosynthetic protein pdxJ
G: Pyridoxal phosphate biosynthetic protein pdxJ
H: Pyridoxal phosphate biosynthetic protein pdxJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,84516
Polymers211,3718
Non-polymers1,4758
Water16,988943
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Pyridoxal phosphate biosynthetic protein pdxJ
F: Pyridoxal phosphate biosynthetic protein pdxJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3665
Polymers52,8432
Non-polymers5233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-29 kcal/mol
Surface area18900 Å2
MethodPISA
3
A: Pyridoxal phosphate biosynthetic protein pdxJ
E: Pyridoxal phosphate biosynthetic protein pdxJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3665
Polymers52,8432
Non-polymers5233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-30 kcal/mol
Surface area18920 Å2
MethodPISA
4
B: Pyridoxal phosphate biosynthetic protein pdxJ
G: Pyridoxal phosphate biosynthetic protein pdxJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2714
Polymers52,8432
Non-polymers4282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-19 kcal/mol
Surface area19310 Å2
MethodPISA
5
D: Pyridoxal phosphate biosynthetic protein pdxJ
H: Pyridoxal phosphate biosynthetic protein pdxJ


Theoretical massNumber of molelcules
Total (without water)52,8432
Polymers52,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-17 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.007, 129.404, 176.088
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
Pyridoxal phosphate biosynthetic protein pdxJ / PNP synthase / pyridoxine 5'-phosphate


Mass: 26421.340 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PDXJ / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A794
#2: Chemical
ChemComp-DXP / 1-DEOXY-D-XYLULOSE-5-PHOSPHATE


Mass: 214.110 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C5H11O7P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, PEG 1000, glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG80001reservoir
210 %PEG10001reservoir
312 mg/mlprotein1drop
44 mMdXP1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2000
RadiationMonochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. all: 163858 / Num. obs: 157249 / % possible obs: 96 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 18.8
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.6 / Num. unique all: 13719 / Rsym value: 0.304 / % possible all: 84.4
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 96 % / Num. measured all: 494561
Reflection shell
*PLUS
% possible obs: 84.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HO4

1ho4


Resolution: 1.96→6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 15691 -random
Rwork0.195 ---
obs0.236 135847 96 %-
all-163858 --
Displacement parametersBiso mean: 20.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.96→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14696 0 88 943 15727
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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