[English] 日本語
Yorodumi
- PDB-3f4n: Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein Pdx... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f4n
TitleCrystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis
ComponentsPyridoxine 5'-phosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / TIM barrel / Octamer / Pyridoxine biosynthesis / CSGID / Structural Genomics / Structural Genomics of National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / NPPSFA / National Project on Protein Structural and Functional Analyses
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
PYRIDOXINE-5'-PHOSPHATE / Pyridoxine 5'-phosphate synthase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsKim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2008
Title: Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis
Authors: Kim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)215,10219
Polymers212,8218
Non-polymers2,28111
Water12,016667
1
A: Pyridoxine 5'-phosphate synthase
B: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7044
Polymers53,2052
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-18 kcal/mol
Surface area19440 Å2
MethodPISA
2
C: Pyridoxine 5'-phosphate synthase
D: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8005
Polymers53,2052
Non-polymers5943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-38 kcal/mol
Surface area19410 Å2
MethodPISA
3
E: Pyridoxine 5'-phosphate synthase
F: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8966
Polymers53,2052
Non-polymers6904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-54 kcal/mol
Surface area18940 Å2
MethodPISA
4
G: Pyridoxine 5'-phosphate synthase
H: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7044
Polymers53,2052
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-19 kcal/mol
Surface area19330 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.627, 114.818, 154.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Pyridoxine 5'-phosphate synthase / E.C.2.6.99.2 / Pyridoxal Phosphate Biosynthetic Protein PdxJ / PNP synthase


Mass: 26602.621 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Description: N-terminal His-tag with TEV protease cut-site / Gene: pdxJ, y1300, YPO2930, YP_2525 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: Q8ZCP4, pyridoxine 5'-phosphate synthase
#2: Chemical
ChemComp-PXP / PYRIDOXINE-5'-PHOSPHATE


Mass: 249.158 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H12NO6P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Magnesium sulfate heptahydrate, 20% w/v Polyethylene glycol 3,350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 9, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.402→34.81 Å / Num. all: 75718 / Num. obs: 75718 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 42.08 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 7.3
Reflection shellResolution: 2.402→2.44 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3435 / % possible all: 88.7

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
BALBESphasing
REFMAC5.4refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1N5W

1n5w


Resolution: 2.402→34.81 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.893 / SU B: 21.15 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.632 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3763 5 %RANDOM
Rwork0.191 ---
all0.195 71176 --
obs0.195 71176 94.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.632 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å20 Å2
2--2.58 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.402→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14621 0 143 667 15431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215132
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.96620544
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47551955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56723.532671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.486152567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.94615143
X-RAY DIFFRACTIONr_chiral_restr0.1140.22417
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.791.59675
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.467215515
X-RAY DIFFRACTIONr_scbond_it2.58635457
X-RAY DIFFRACTIONr_scangle_it4.1884.55029
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 240 -
Rwork0.272 4704 -
obs-4944 86.22 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8084-0.28680.17211.02560.52921.2409-0.0146-0.0189-0.13510.06770.062200.10570.0099-0.04760.0456-0.0090.0080.0583-0.00750.051330.94338.276211.0447
21.55250.00870.53440.9242-0.23520.7394-0.0448-0.20560.0720.01940.01180.0803-0.0071-0.15120.0330.02430.02440.00630.147-0.00970.02550.269827.970317.7246
31.99260.1616-0.05071.07270.1410.3891-0.03220.1175-0.2337-0.02170.1077-0.1337-0.01580.0466-0.07550.04720.00080.00810.0976-0.08120.073957.548335.231717.7032
40.45390.09020.11231.1248-0.131.0704-0.11570.10160.1142-0.04810.03370.0421-0.1634-0.01570.0820.073-0.0041-0.03950.07040.03850.071927.706949.85962.7402
51.3209-0.04950.25231.45360.21610.29660.0125-0.09480.23370.0448-0.04360.0947-0.0037-0.03020.03110.06270.00770.02310.0592-0.06440.093133.101263.812837.5103
61.814-0.6854-0.0311.09450.02410.9186-0.0209-0.22780.1270.07610.072-0.150.06740.0244-0.05110.06380.0072-0.01980.0491-0.03520.048249.125134.945454.7791
71.3385-0.28720.01011.27540.14411.00750.0126-0.17950.15220.026-0.05910.2463-0.0036-0.26090.04650.02490.01910.02060.2074-0.06370.08866.836940.789952.9152
81.1454-0.34440.25030.9844-0.47950.685-0.0218-0.1252-0.10040.01610.0830.0097-0.0065-0.1015-0.06120.041-0.0152-0.00150.12850.06420.033122.92178.086148.2804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 243
2X-RAY DIFFRACTION2B2 - 243
3X-RAY DIFFRACTION3C1 - 243
4X-RAY DIFFRACTION4D2 - 243
5X-RAY DIFFRACTION5E3 - 243
6X-RAY DIFFRACTION6F2 - 243
7X-RAY DIFFRACTION7G2 - 243
8X-RAY DIFFRACTION8H3 - 243

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more