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- PDB-3gk0: Crystal structure of pyridoxal phosphate biosynthetic protein fro... -

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Basic information

Entry
Database: PDB / ID: 3gk0
TitleCrystal structure of pyridoxal phosphate biosynthetic protein from Burkholderia pseudomallei
ComponentsPyridoxine 5'-phosphate synthase
KeywordsTRANSFERASE / deCODE / SSGCID / NIAID / SBRI / Pyridoxine biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / cytoplasm
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 speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: 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 / 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_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

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Assembly

Deposited unit
A: Pyridoxine 5'-phosphate synthase
B: Pyridoxine 5'-phosphate synthase
C: Pyridoxine 5'-phosphate synthase
D: Pyridoxine 5'-phosphate synthase
E: Pyridoxine 5'-phosphate synthase
F: Pyridoxine 5'-phosphate synthase
G: Pyridoxine 5'-phosphate synthase
H: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,82016
Polymers238,7038
Non-polymers1,1178
Water15,331851
1
A: Pyridoxine 5'-phosphate synthase
D: Pyridoxine 5'-phosphate synthase
F: Pyridoxine 5'-phosphate synthase
G: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9708
Polymers119,3514
Non-polymers6184
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-81 kcal/mol
Surface area36120 Å2
MethodPISA
2
A: Pyridoxine 5'-phosphate synthase
G: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9854
Polymers59,6762
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-30 kcal/mol
Surface area19490 Å2
MethodPISA
3
B: Pyridoxine 5'-phosphate synthase
C: Pyridoxine 5'-phosphate synthase
E: Pyridoxine 5'-phosphate synthase
H: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8508
Polymers119,3514
Non-polymers4994
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-87 kcal/mol
Surface area36240 Å2
MethodPISA
4
B: Pyridoxine 5'-phosphate synthase
E: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8664
Polymers59,6762
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-35 kcal/mol
Surface area19570 Å2
MethodPISA
5
C: Pyridoxine 5'-phosphate synthase
H: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9854
Polymers59,6762
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-32 kcal/mol
Surface area19300 Å2
MethodPISA
6
D: Pyridoxine 5'-phosphate synthase
F: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9854
Polymers59,6762
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-31 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 91.864, 90.024
Angle α, β, γ (deg.)118.480, 116.810, 93.500
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 29837.867 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: pdxJ / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JQ80, pyridoxine 5'-phosphate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-DXP / 1-DEOXY-D-XYLULOSE-5-PHOSPHATE / 1-Deoxy-D-xylulose 5-phosphate


Mass: 214.110 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H11O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16.4% PEG4000, 0.1 M Hepes NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97934 Å
DetectorDetector: CCD / Date: Dec 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 91137 / % possible obs: 96.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.107 / Χ2: 1.069 / Net I/σ(I): 12.627
Reflection shellResolution: 2.28→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8058 / Χ2: 0.901 / % possible all: 85.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M5W

1m5w


Resolution: 2.28→46.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.839 / SU B: 6.952 / SU ML: 0.17 / SU R Cruickshank DPI: 0.359 / SU Rfree: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.36 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4580 5 %RANDOM
Rwork0.186 ---
obs0.189 91104 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.66 Å2 / Biso mean: 28.325 Å2 / Biso min: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20.93 Å2-0.84 Å2
2--0.49 Å2-0.65 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.28→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14763 0 64 851 15678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02115131
X-RAY DIFFRACTIONr_bond_other_d0.0010.029812
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.94720620
X-RAY DIFFRACTIONr_angle_other_deg0.894323832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37551984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40623.057700
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.597152333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.24215158
X-RAY DIFFRACTIONr_chiral_restr0.0650.22428
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023053
X-RAY DIFFRACTIONr_mcbond_it0.4691.59827
X-RAY DIFFRACTIONr_mcbond_other0.0771.54011
X-RAY DIFFRACTIONr_mcangle_it0.91215669
X-RAY DIFFRACTIONr_scbond_it1.38935304
X-RAY DIFFRACTIONr_scangle_it2.4234.54942
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 186 -
Rwork0.261 3766 -
all-3952 -
obs--55.1 %

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