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- PDB-3o6c: Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter ... -

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Basic information

Entry
Database: PDB / ID: 3o6c
TitlePyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni
ComponentsPyridoxine 5'-phosphate synthase
KeywordsTRANSFERASE / structural genomics / IDP90671 / Center for Structural Genomics of Infectious Diseases / CSGID / pyridoxine synthesis / Vitamin B6 / pyridoxal phosphate / PdxJ
Function / homology
Function and homology information


pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / 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
PHOSPHATE ION / Pyridoxine 5'-phosphate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsOsipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni.
Authors: Osipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 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 / struct_site
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 / _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: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6593
Polymers29,4691
Non-polymers1902
Water5,386299
1
A: Pyridoxine 5'-phosphate synthase
hetero molecules

A: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3176
Polymers58,9382
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area4200 Å2
ΔGint-53 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.976, 90.976, 155.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Pyridoxine 5'-phosphate synthase / PNP synthase


Mass: 29468.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj1238, pdxJ / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9PN59, pyridoxine 5'-phosphate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.056 M sodium phosphate, 1.344 di-potassium phosphate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.87→49.6 Å / Num. all: 27387 / Num. obs: 27387 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.1 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.101 / Χ2: 1.886 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.87-1.918.30.8516.113461.718100
1.9-1.9418.40.56213371.394100
1.94-1.9718.40.50613601.382100
1.97-2.0118.40.39513371.319100
2.01-2.0618.40.36113471.433100
2.06-2.1118.30.33113491.876100
2.11-2.1618.60.26413381.337100
2.16-2.2218.50.22713641.377100
2.22-2.2818.60.20113511.436100
2.28-2.3618.50.17513511.436100
2.36-2.4418.50.15413621.458100
2.44-2.5418.50.13813531.6100
2.54-2.6518.50.12113581.611100
2.65-2.7918.40.10913661.827100
2.79-2.9718.30.10313792.183100
2.97-3.2180.0913702.738100
3.2-3.5217.70.07513872.961100
3.52-4.0317.30.05814032.855100
4.03-5.0717.10.04914252.826100
5.07-5016.10.05215043.07999.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→49.7 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.688 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 1368 5 %RANDOM
Rwork0.1438 ---
all0.1453 27296 --
obs0.1453 27296 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.79 Å2 / Biso mean: 23.431 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.87→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 10 299 2361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222252
X-RAY DIFFRACTIONr_bond_other_d0.0010.021556
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.983062
X-RAY DIFFRACTIONr_angle_other_deg0.99333870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05825.856111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02815463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8771511
X-RAY DIFFRACTIONr_chiral_restr0.110.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_mcbond_it0.9031.51366
X-RAY DIFFRACTIONr_mcbond_other0.291.5549
X-RAY DIFFRACTIONr_mcangle_it1.67422223
X-RAY DIFFRACTIONr_scbond_it2.9083886
X-RAY DIFFRACTIONr_scangle_it4.9134.5819
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 93 -
Rwork0.179 1839 -
all-1932 -
obs-1932 97.67 %
Refinement TLS params.Method: refined / Origin x: 17.9073 Å / Origin y: 41.116 Å / Origin z: 17.3929 Å
111213212223313233
T0.0052 Å20.0017 Å20.0027 Å2-0.0347 Å20.0064 Å2--0.0125 Å2
L0.3612 °20.0353 °2-0.2591 °2-0.4013 °2-0.0368 °2--0.6274 °2
S0.0023 Å °-0.0484 Å °0.0024 Å °0.0461 Å °-0.0046 Å °0.0209 Å °-0.004 Å °0.0187 Å °0.0023 Å °

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