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- PDB-2iss: Structure of the PLP synthase Holoenzyme from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 2iss
TitleStructure of the PLP synthase Holoenzyme from Thermotoga maritima
Components
  • Glutamine amidotransferase subunit pdxT
  • Pyridoxal biosynthesis lyase pdxS
KeywordsLYASE / TRANSFERASE / (beta/alpha)8-barrel / alpha/beta three layer sandwich
Function / homology
Function and homology information


pyridoxine metabolic process / vitamin B6 biosynthetic process / glutaminase complex / amine-lyase activity / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / glutamine catabolic process / pyridoxine biosynthetic process / glutaminase ...pyridoxine metabolic process / vitamin B6 biosynthetic process / glutaminase complex / amine-lyase activity / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / glutamine catabolic process / pyridoxine biosynthetic process / glutaminase / glutaminase activity / amino acid metabolic process / cytosol
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. ...Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / PHOSPHATE ION / Pyridoxal 5'-phosphate synthase subunit PdxT / Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZein, F. / Zhang, Y. / Kang, Y.N. / Burns, K. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Insights into the Mechanism of the PLP Synthase Holoenzyme from Thermotoga maritima
Authors: Zein, F. / Zhang, Y. / Kang, Y.N. / Burns, K. / Begley, T.P. / Ealick, S.E.
History
DepositionOct 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_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

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Assembly

Deposited unit
A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Glutamine amidotransferase subunit pdxT
E: Glutamine amidotransferase subunit pdxT
F: Glutamine amidotransferase subunit pdxT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,13912
Polymers173,1646
Non-polymers9756
Water68538
1
A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Glutamine amidotransferase subunit pdxT
E: Glutamine amidotransferase subunit pdxT
F: Glutamine amidotransferase subunit pdxT
hetero molecules

A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Glutamine amidotransferase subunit pdxT
E: Glutamine amidotransferase subunit pdxT
F: Glutamine amidotransferase subunit pdxT
hetero molecules

A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Glutamine amidotransferase subunit pdxT
E: Glutamine amidotransferase subunit pdxT
F: Glutamine amidotransferase subunit pdxT
hetero molecules

A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Glutamine amidotransferase subunit pdxT
E: Glutamine amidotransferase subunit pdxT
F: Glutamine amidotransferase subunit pdxT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)696,55648
Polymers692,65524
Non-polymers3,90124
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area89290 Å2
ΔGint-329 kcal/mol
Surface area179160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.529, 204.098, 221.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-380-

HOH

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Components

#1: Protein Pyridoxal biosynthesis lyase pdxS


Mass: 34345.121 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: DSM3109 / Gene: pdxS / Plasmid: pCLK1540 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q9WYU4, Lyases
#2: Protein Glutamine amidotransferase subunit pdxT / Glutamine amidotransferase glutaminase subunit pdxT


Mass: 23376.123 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: DSM3109 / Gene: pdxT / Plasmid: pCLK1541 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q9WYU3, EC: 2.6.-.-
#3: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11O8P
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.8M disodium hydrogen phosphate, 1.2M potassium dihydrogen phosphate, 0.2M lithium sulfate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2005
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 46860 / Num. obs: 45755 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.087 / Net I/σ(I): 14.33
Reflection shellResolution: 2.9→3 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.14 / Num. unique all: 4579 / Rsym value: 0.456 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZNN

1znn


Resolution: 2.9→46.34 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 167445.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2178 5 %RANDOM
Rwork0.213 ---
all0.257 46848 --
obs0.213 43430 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.7735 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 52.6 Å2
Baniso -1Baniso -2Baniso -3
1-15.01 Å20 Å20 Å2
2---8.94 Å20 Å2
3----6.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10768 0 54 38 10860
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 326 4.8 %
Rwork0.312 6504 -
obs-6504 88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_lyp_061906_2.paramprotein_lyp_061906_2.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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