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- PDB-2nv2: Structure of the PLP synthase complex Pdx1/2 (YaaD/E) from Bacill... -

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Basic information

Entry
Database: PDB / ID: 2nv2
TitleStructure of the PLP synthase complex Pdx1/2 (YaaD/E) from Bacillus subtilis
Components
  • Glutamine amidotransferase subunit pdxT
  • Pyridoxal biosynthesis lyase pdxS
KeywordsLYASE/TRANSFERASE / (beta/alpha)8-barrel / 3-Layer(aba) Sandwich / PLP synthase complex / LYASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


pyridoxine metabolic process / amine-lyase activity / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / glutamine catabolic process / glutaminase / glutaminase activity ...pyridoxine metabolic process / amine-lyase activity / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / glutamine catabolic process / glutaminase / glutaminase activity / amino acid metabolic process / identical protein binding / 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
GLUTAMINE / Pyridoxal 5'-phosphate synthase subunit PdxS / Pyridoxal 5'-phosphate synthase subunit PdxT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsStrohmeier, M. / Tews, I. / Sinning, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of a bacterial pyridoxal 5'-phosphate synthase complex
Authors: Strohmeier, M. / Raschle, T. / Mazurkiewicz, J. / Rippe, K. / Sinning, I. / Fitzpatrick, T.B. / Tews, I.
History
DepositionNov 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Glutamine amidotransferase subunit pdxT
C: Pyridoxal biosynthesis lyase pdxS
D: Glutamine amidotransferase subunit pdxT
E: Pyridoxal biosynthesis lyase pdxS
F: Glutamine amidotransferase subunit pdxT
G: Pyridoxal biosynthesis lyase pdxS
H: Glutamine amidotransferase subunit pdxT
I: Pyridoxal biosynthesis lyase pdxS
J: Glutamine amidotransferase subunit pdxT
K: Pyridoxal biosynthesis lyase pdxS
L: Glutamine amidotransferase subunit pdxT
M: Pyridoxal biosynthesis lyase pdxS
N: Glutamine amidotransferase subunit pdxT
O: Pyridoxal biosynthesis lyase pdxS
P: Glutamine amidotransferase subunit pdxT
Q: Pyridoxal biosynthesis lyase pdxS
R: Glutamine amidotransferase subunit pdxT
S: Pyridoxal biosynthesis lyase pdxS
T: Glutamine amidotransferase subunit pdxT
U: Pyridoxal biosynthesis lyase pdxS
V: Glutamine amidotransferase subunit pdxT
W: Pyridoxal biosynthesis lyase pdxS
X: Glutamine amidotransferase subunit pdxT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)653,30466
Polymers650,00724
Non-polymers3,29642
Water104,0195774
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area84980 Å2
ΔGint-391 kcal/mol
Surface area177540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.507, 259.009, 144.962
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX

#1: Protein
Pyridoxal biosynthesis lyase pdxS / Superoxide-inducible protein 7 / SOI7 / Pdx1


Mass: 31649.562 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: strain 168 / Plasmid: pET21a, pETBsPdx1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 [DE3] / References: UniProt: P37527, Lyases
#2: Protein
Glutamine amidotransferase subunit pdxT / / Glutamine amidotransferase glutaminase subunit pdxT / Pdx2


Mass: 22517.717 Da / Num. of mol.: 12 / Mutation: H170N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: strain 168 / Plasmid: pET24b, pETBsPdx2H170N-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 [DE3] / References: UniProt: P37528, EC: 2.6.-.-

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Non-polymers , 4 types, 5816 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H10N2O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5774 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-17% PEG 4000, 200mM tri-ammonium citrate pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 17, 2005 / Details: ESRF
RadiationMonochromator: ESRF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 388915 / Num. obs: 381798 / % possible obs: 98.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 29 Å2 / Rsym value: 0.081 / Net I/σ(I): 12
Reflection shellResolution: 2.12→2.14 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.443 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NV1
Resolution: 2.12→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.636 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19789 19065 5 %RANDOM
Rwork0.14608 ---
obs0.14868 361794 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.093 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20.31 Å2
2---0.43 Å20 Å2
3----0.49 Å2
Refine analyzeLuzzati coordinate error obs: 0.225 Å
Refinement stepCycle: LAST / Resolution: 2.12→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41883 0 203 5774 47860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02243133
X-RAY DIFFRACTIONr_bond_other_d0.0020.0229288
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.97358269
X-RAY DIFFRACTIONr_angle_other_deg0.959371772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24655665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26224.6551912
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.956157682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.12315313
X-RAY DIFFRACTIONr_chiral_restr0.0890.26701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0248547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028182
X-RAY DIFFRACTIONr_nbd_refined0.2230.29638
X-RAY DIFFRACTIONr_nbd_other0.2150.233501
X-RAY DIFFRACTIONr_nbtor_refined0.1750.220898
X-RAY DIFFRACTIONr_nbtor_other0.0870.223371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.23942
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1010.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0431.530147
X-RAY DIFFRACTIONr_mcbond_other0.1861.511466
X-RAY DIFFRACTIONr_mcangle_it1.383244402
X-RAY DIFFRACTIONr_scbond_it2.318316164
X-RAY DIFFRACTIONr_scangle_it3.4694.513799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 1321 -
Rwork0.194 26337 -
obs--96.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.24140.0697-0.04390.2878-0.11370.58310.0084-0.0273-0.04080.0426-0.0197-0.039-0.13780.10830.0112-0.0719-0.0549-0.020.01770-0.012924.605536.155948.2131
21.46860.05430.0482.0056-0.12711.75320.0317-0.10780.2646-0.0304-0.0079-0.0666-0.60310.1819-0.02380.1241-0.1851-0.0099-0.1367-0.0483-0.090631.07262.263251.1467
30.38750.1775-0.03330.27480.05530.45270.0018-0.01470.0086-0.0135-0.0116-0.0363-0.03650.07420.0098-0.086-0.00480.00930.0140.00820.002722.093229.168110.0046
41.37340.0508-0.41441.69070.3322.2740.07780.29450.3092-0.3711-0.0006-0.0584-0.322-0.0437-0.0772-0.0006-0.02980.0367-0.01820.1297-0.066525.795245.1974-11.5458
50.07370.1508-0.13120.7683-0.04160.3453-0.009-0.02050.0368-0.1043-0.0068-0.1520.08150.03140.0159-0.05670.02910.0434-0.0161-0.00030.023817.7502-7.1177-2.7651
61.54-0.1332-0.29241.57250.0432.6537-0.13690.3436-0.144-0.41210.0176-0.1370.5146-0.18540.11930.1712-0.03790.1492-0.0711-0.0619-0.186618.7556-17.5632-27.4497
70.1112-0.099-0.09850.3615-0.04520.53860.00360.01640.0556-0.0134-0.0068-0.05010.08980.06640.0031-0.03840.03170.01-0.0092-0.0141-0.015216.007-36.399522.6286
80.8531-0.03790.0111.674-0.01172.0916-0.0098-0.0063-0.10950.11290.05710.01080.5169-0.0377-0.04730.1330.05310.0205-0.1388-0.0126-0.097316.4709-63.079119.2759
90.2494-0.21390.06010.42710.19090.3912-0.00180.03810.0110.03470.0038-0.06320.03320.0509-0.002-0.04340.0068-0.0021-0.0163-0.0143-0.000318.7551-29.28460.8584
100.9360.10240.33571.46480.31611.5922-0.0153-0.1387-0.11820.3740.0165-0.00830.2431-0.0339-0.00130.06340.0369-0.0167-0.09280.039-0.063520.7649-45.72682.1587
110.0759-0.00860.16830.7535-0.01250.3733-0.03850.0554-0.02110.08760.0241-0.1467-0.01420.0650.0144-0.0829-0.0121-0.043-0.0086-0.01070.034722.93996.97273.5692
121.40460.5666-0.01342.73770.24911.51210.0483-0.21740.0810.6637-0.0752-0.2025-0.21140.09610.02690.0919-0.0251-0.1794-0.074-0.0302-0.086328.228417.112597.9872
130.1107-0.10690.10410.29570.02490.45-0.011-0.0046-0.04860.02370.00940.0304-0.0628-0.04990.0016-0.05380.02730.00320.0094-0.0047-0.0174-20.05140.887225.1608
140.6908-0.07130.01321.83450.25231.3756-0.0689-0.01250.06430.0360.1048-0.0419-0.41310.0493-0.03590.07210.0341-0.0208-0.0898-0.0142-0.1004-20.308767.619622.3455
150.1967-0.1447-0.06670.4151-0.15630.45740.00540.063-0.00210.06210.00530.0419-0.0829-0.0481-0.0107-0.0440.01860.0105-0.0102-0.0011-0.0172-18.932333.180563.0868
160.98960.1268-0.10872.0234-0.33331.7256-0.0099-0.09880.13860.5591-0.0133-0.0556-0.17410.08010.02320.16860.0490.0028-0.13-0.0329-0.127-19.395549.055684.93
170.15520.0167-0.14690.52640.18490.4453-0.00630.06640.03650.0818-0.05930.0740.0517-0.08810.0656-0.0598-0.02630.0368-0.014-0.03710.009-22.1039-3.468575.5377
181.32330.2075-0.19941.3441-0.06351.7537-0.0482-0.2237-0.1110.2806-0.05850.02850.3350.01130.10670.103-0.04560.1102-0.0721-0.0127-0.1327-25.2655-14.0216100.3015
190.18760.1409-0.05120.39720.12320.6538-0.0014-0.00190.07640.0503-0.03090.08980.1271-0.10670.0323-0.0623-0.06210.02740.0019-0.04180.0009-26.128-32.333849.9222
201.64290.24170.22882.08150.3562.09110.0471-0.0273-0.29480.0784-0.03460.070.6374-0.1419-0.01250.1313-0.16890.0656-0.1596-0.0094-0.0694-31.6514-58.579253.2123
210.23210.05970.06530.6149-0.22410.44720.0081-0.0195-0.0083-0.11730.03650.13630.1147-0.0611-0.0446-0.0698-0.0451-0.0454-0.0115-0.00960.0136-27.313-24.647112.0475
222.12680.13190.52862.1549-0.4862.78130.07260.382-0.3803-0.71520.05750.32890.5070.027-0.13010.1851-0.0898-0.2028-0.1167-0.1369-0.0874-33.2868-40.2253-9.3206
230.2295-0.07920.13510.3821-0.04890.27170.0042-0.0074-0.0225-0.03520.01460.0450.0105-0.0499-0.0188-0.07730.0055-0.01640.0175-0.0098-0.0046-24.39311.999-0.2558
240.8834-0.3308-0.08842.0414-0.12271.20730.02220.14510.039-0.4390.01750.0183-0.1279-0.0538-0.03970.02580.0028-0.0464-0.0040.0041-0.1298-27.994823.1207-24.7055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2692 - 269
2X-RAY DIFFRACTION2BB1 - 1931 - 193
3X-RAY DIFFRACTION3CC2 - 2702 - 270
4X-RAY DIFFRACTION4DD1 - 1931 - 193
5X-RAY DIFFRACTION5EE2 - 2702 - 270
6X-RAY DIFFRACTION6FF1 - 1911 - 191
7X-RAY DIFFRACTION7GG2 - 2692 - 269
8X-RAY DIFFRACTION8HH1 - 1931 - 193
9X-RAY DIFFRACTION9II2 - 2722 - 272
10X-RAY DIFFRACTION10JJ1 - 1931 - 193
11X-RAY DIFFRACTION11KK2 - 2712 - 271
12X-RAY DIFFRACTION12LL1 - 1921 - 192
13X-RAY DIFFRACTION13MM2 - 2702 - 270
14X-RAY DIFFRACTION14NN1 - 1931 - 193
15X-RAY DIFFRACTION15OO2 - 2692 - 269
16X-RAY DIFFRACTION16PP1 - 1931 - 193
17X-RAY DIFFRACTION17QQ2 - 2712 - 271
18X-RAY DIFFRACTION18RR1 - 1931 - 193
19X-RAY DIFFRACTION19SS2 - 2712 - 271
20X-RAY DIFFRACTION20TT1 - 1931 - 193
21X-RAY DIFFRACTION21UU2 - 2722 - 272
22X-RAY DIFFRACTION22VV1 - 1931 - 193
23X-RAY DIFFRACTION23WW2 - 2712 - 271
24X-RAY DIFFRACTION24XX1 - 1931 - 193

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