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- PDB-2zbt: Crystal structure of pyridoxine biosynthesis protein from Thermus... -

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Basic information

Entry
Database: PDB / ID: 2zbt
TitleCrystal structure of pyridoxine biosynthesis protein from Thermus thermophilus HB8
ComponentsPyridoxal biosynthesis lyase pdxS
KeywordsLYASE / Pyridoxine biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsManzoku, M. / Ebihara, A. / Fujimoto, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of pyridoxine biosynthesis protein from Thermus thermophilus HB8
Authors: Manzoku, M. / Ebihara, A. / Fujimoto, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionOct 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Pyridoxal biosynthesis lyase pdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2518
Polymers129,7784
Non-polymers4734
Water11,205622
1
A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Pyridoxal biosynthesis lyase pdxS
hetero molecules

A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Pyridoxal biosynthesis lyase pdxS
hetero molecules

A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Pyridoxal biosynthesis lyase pdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,75324
Polymers389,33412
Non-polymers1,41812
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area52260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.970, 180.970, 100.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Pyridoxal biosynthesis lyase pdxS


Mass: 32444.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: pdxS / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKD9*PLUS, Lyases
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT. THIS SEQUENCE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.1M Magnesium acetate, 0.1M Sodium cacodylate pH6.7, 22.5% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B210.97904, 0.9000, 0.97942
SYNCHROTRONSPring-8 BL26B221
Detector
TypeIDDetectorDate
RIGAKU JUPITER 2101CCDDec 9, 2005
RIGAKU JUPITER 2102CCDMay 22, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI Double-CrystalMADMx-ray1
2SI Double-CrystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
20.91
30.979421
411
ReflectionResolution: 1.65→50 Å / Num. obs: 148066 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 52.73
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→47.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3622417.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 14786 10 %RANDOM
Rwork0.194 ---
obs0.194 148028 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.243 Å2 / ksol: 0.367913 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å21.11 Å20 Å2
2--0.53 Å20 Å2
3----1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.65→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8318 0 32 622 8972
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 2408 9.8 %
Rwork0.215 22267 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3mpd_xplor.parammpd_xplor.top

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