[English] 日本語
Yorodumi
- PDB-6rg0: Structure of pdxj -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rg0
TitleStructure of pdxj
ComponentsPyridoxine 5'-phosphate synthase
KeywordsTRANSFERASE / Serine phosphatase SerB / serine aminotransferase SerC / histidinol phosphatase HisB / histidinol phosphatase aminotransferase HisC
Function / homology
Function and homology information


pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / identical protein binding / 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 synthase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.074 Å
AuthorsRohweder, B. / Rajendran, C. / Sterner, R.
Funding support1items
OrganizationGrant numberCountry
German Research Foundation
CitationJournal: Biochemistry / Year: 2019
Title: Library Selection with a Randomized Repertoire of ( beta alpha )8-Barrel Enzymes Results in Unexpected Induction of Gene Expression.
Authors: Rohweder, B. / Lehmann, G. / Eichner, N. / Polen, T. / Rajendran, C. / Ruperti, F. / Linde, M. / Treiber, T. / Jung, O. / Dettmer, K. / Meister, G. / Bott, M. / Gronwald, W. / Sterner, R.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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


Theoretical massNumber of molelcules
Total (without water)116,9074
Polymers116,9074
Non-polymers00
Water00
1
A: Pyridoxine 5'-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)29,2271
Polymers29,2271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyridoxine 5'-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)29,2271
Polymers29,2271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pyridoxine 5'-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)29,2271
Polymers29,2271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pyridoxine 5'-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)29,2271
Polymers29,2271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.050, 188.124, 192.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 29226.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: pdxJ, b2564, JW2548 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A794, pyridoxine 5'-phosphate synthase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.0744→48.44 Å / Num. all: 373532 / Num. obs: 27529 / % possible obs: 99.3 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1137 / Rpim(I) all: 0.03076 / Rrim(I) all: 0.1137 / Net I/σ(I): 23.01
Reflection shellResolution: 3.074→3.184 Å / Redundancy: 14 % / Rmerge(I) obs: 1.086 / Num. unique obs: 2544 / CC1/2: 0.801 / Rpim(I) all: 0.2978 / Rrim(I) all: 1.127

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HO1, 1M5W
Resolution: 3.074→48.438 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.88
RfactorNum. reflection% reflection
Rfree0.2485 1367 5.01 %
Rwork0.1821 --
obs0.1854 27345 99.01 %
all-51807 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.074→48.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6975 0 0 0 6975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017081
X-RAY DIFFRACTIONf_angle_d1.2419584
X-RAY DIFFRACTIONf_dihedral_angle_d13.0624337
X-RAY DIFFRACTIONf_chiral_restr0.061157
X-RAY DIFFRACTIONf_plane_restr0.0081257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0744-3.13030.37721270.33572212X-RAY DIFFRACTION86
3.1303-3.19050.29341380.28972658X-RAY DIFFRACTION100
3.1905-3.25560.38451360.27292571X-RAY DIFFRACTION100
3.2556-3.32640.32671430.26332650X-RAY DIFFRACTION100
3.3264-3.40370.30261410.26332597X-RAY DIFFRACTION100
3.4037-3.48880.32111400.23072596X-RAY DIFFRACTION100
3.4888-3.58310.32741340.22872610X-RAY DIFFRACTION100
3.5831-3.68850.29461390.20822607X-RAY DIFFRACTION100
3.6885-3.80750.3151420.18742650X-RAY DIFFRACTION100
3.8075-3.94350.19431310.16932589X-RAY DIFFRACTION100
3.9435-4.10140.23161390.16432623X-RAY DIFFRACTION100
4.1014-4.28790.22271340.15732597X-RAY DIFFRACTION100
4.2879-4.51380.19181330.13932615X-RAY DIFFRACTION100
4.5138-4.79640.2231360.142593X-RAY DIFFRACTION100
4.7964-5.16630.18391380.14542618X-RAY DIFFRACTION100
5.1663-5.68550.28951440.1742639X-RAY DIFFRACTION100
5.6855-6.50660.28741350.20212586X-RAY DIFFRACTION100
6.5066-8.19110.2461380.17652588X-RAY DIFFRACTION99
8.1911-48.44370.20171360.15882614X-RAY DIFFRACTION99
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)
12.37461.89850.00471.69160.24362.27780.01390.1175-0.2305-0.21330.0723-0.3930.34740.38660.00020.59550.05450.09060.51260.02590.431824.5696-7.3679-23.1944
21.7228-1.68210.80032.12440.17823.2057-0.04910.6050.2459-0.40990.19010.170.09330.0850.00040.6746-0.04390.05180.61560.0020.402226.077-5.0823-35.4542
30.2052-0.0265-0.24120.2084-0.08370.36940.37330.3030.4142-0.8154-0.26320.19630.47930.1046-0.00060.65420.0115-0.05070.99240.02220.436131.5422.9956-45.7858
40.37390.2454-0.89881.81380.74491.4429-0.26170.32160.1263-0.21110.1023-0.3073-0.11350.00550.00060.4848-0.00450.02330.54610.06820.474932.402810.5982-34.4917
51.92830.9938-0.61750.792-0.37280.30050.1358-0.03290.1170.0192-0.03730.1825-0.17560.06720.00020.52120.04020.06160.46730.09590.375728.740712.244-23.939
60.4331-0.1765-0.02030.50920.73610.7304-0.1737-0.0310.6060.5043-0.06060.4012-0.03-0.1967-0.00220.48350.06330.05440.43610.15640.610318.86428.6969-15.5103
72.1631-0.38030.01093.21880.43721.6197-0.07020.1076-0.2845-0.1899-0.495-0.42050.28310.6101-0.00410.37620.09860.090.63770.27890.54439.2643-10.1499-4.6252
80.95990.98450.34631.2855-0.3731.6170.22420.37410.21150.1037-0.8146-0.4451.13930.9108-0.08340.7680.50580.27660.9590.46871.020848.0816-27.4767-2.3011
92.06390.30121.43981.82850.12761.51730.0103-0.0507-0.4591-0.1678-0.07840.25610.789-0.0192-0.00510.66210.08810.09740.41440.170.570827.6809-25.9682-2.5703
100.3509-0.4344-0.30631.06340.87750.8770.2047-0.267-0.4304-0.96920.49370.72390.7881-0.8686-0.00020.5086-0.0957-0.08730.66420.18980.70312.7813-16.4873-18.7053
110.6816-0.162-0.37961.8461-0.33271.1690.13120.0761-0.3777-0.5059-0.0256-0.23980.1705-0.428-0.00010.8014-0.0961-0.02910.73360.04050.67187.3009-22.4873-22.5809
120.5538-0.9752-1.31821.66770.97272.5191-0.31330.3259-0.6463-0.60090.25440.04160.7722-0.3012-0.00041.1763-0.2051-0.08340.80470.05091.0170.5481-39.6005-22.9071
130.4862-0.33230.42420.3143-0.35540.2818-0.20310.3614-1.13060.1736-0.04680.31621.0477-0.34090.00560.9672-0.18310.23630.73820.28621.2587-5.4801-36.6141-5.8207
140.86591.06350.52331.02780.57040.5685-0.1073-0.2053-0.1266-0.18190.33590.08740.2296-0.4696-0.00010.771-0.09460.01610.63740.22990.90940.8076-27.0673-6.4854
150.2493-0.1647-0.040.13190.02410.2376-0.1562-0.13530.08491.01050.44870.11750.1775-0.2343-0.00040.8349-0.0334-0.02930.63840.19180.56916.685-21.3685-1.5455
16-0.0142-0.24160.13011.5564-1.07270.4804-0.0014-0.41030.05821.52740.74350.2945-1.2508-1.31580.0480.60790.06480.14951.06150.21151.2265-10.97092.2289-10.0761
170.06870.09620.0610.13390.0252-0.0338-0.18871.3569-0.03910.46360.09820.16130.5338-0.6468-0.00161.11620.0802-0.011.89650.11781.0998-24.88161.8881-19.3487
180.70870.17920.24310.6584-0.32830.2818-0.47440.331-0.79020.04970.31270.07630.42970.2719-0.00061.00550.21990.26021.415-0.04351.5817-19.08634.613-24.1359
190.02720.0695-0.08040.2405-0.24490.1412-0.4706-0.0087-0.2879-0.841.10810.22931.5391-1.0264-0.01031.26840.3418-0.23722.5992-0.10171.3519-24.99179.521-30.6158
200.64830.16261.23990.81641.29092.4020.3020.30480.8658-0.64430.031-0.2195-0.3973-0.67390.00290.95680.25540.05591.1660.48571.0297-8.575812.0892-28.4465
210.95480.2746-0.160.2402-0.43071.0442-0.06110.76690.64690.0343-0.5475-1.9619-0.32540.48770.00070.6510.0035-0.07660.7060.25991.02220.34995.768-15.8933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 177 )
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 239 )
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 256 )
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 89 )
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 167 )
9X-RAY DIFFRACTION9chain 'B' and (resid 168 through 256 )
10X-RAY DIFFRACTION10chain 'C' and (resid 15 through 39 )
11X-RAY DIFFRACTION11chain 'C' and (resid 40 through 89 )
12X-RAY DIFFRACTION12chain 'C' and (resid 90 through 160 )
13X-RAY DIFFRACTION13chain 'C' and (resid 161 through 197 )
14X-RAY DIFFRACTION14chain 'C' and (resid 198 through 239 )
15X-RAY DIFFRACTION15chain 'C' and (resid 240 through 256 )
16X-RAY DIFFRACTION16chain 'D' and (resid 15 through 81 )
17X-RAY DIFFRACTION17chain 'D' and (resid 82 through 98 )
18X-RAY DIFFRACTION18chain 'D' and (resid 99 through 116 )
19X-RAY DIFFRACTION19chain 'D' and (resid 117 through 135 )
20X-RAY DIFFRACTION20chain 'D' and (resid 136 through 218 )
21X-RAY DIFFRACTION21chain 'D' and (resid 219 through 256 )

+
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://pdbjlvh1.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