[English] 日本語
Yorodumi
- PDB-1xub: Structure and function of the phenazine biosynthetic protein PhzF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xub
TitleStructure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens
ComponentsPhenazine biosynthesis protein phzF
KeywordsBIOSYNTHETIC PROTEIN / phenazine biosynthesis
Function / homology
Function and homology information


trans-2,3-dihydro-3-hydroxyanthranilate isomerase / trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity / phenazine biosynthetic process / cytoplasm
Similarity search - Function
Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement of 1U1V / Resolution: 1.3 Å
AuthorsBlankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V.
CitationJournal: PROC.NATL.ACAD.SCI.USA / Year: 2004
Title: Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens
Authors: Blankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenazine biosynthesis protein phzF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2862
Polymers32,1891
Non-polymers961
Water6,467359
1
A: Phenazine biosynthesis protein phzF
hetero molecules

A: Phenazine biosynthesis protein phzF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5714
Polymers64,3792
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565x-y,-y+1,-z+1/31
Unit cell
Length a, b, c (Å)56.128, 56.128, 154.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1021-

HOH

-
Components

#1: Protein Phenazine biosynthesis protein phzF


Mass: 32189.494 Da / Num. of mol.: 1 / Mutation: H74A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q51792
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.2 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 11% (w/v) PEG 3350, 0.1M Na Citrate, 0.2M (NH4)2 Sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 70364 / Num. obs: 63575 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.051 / Net I/σ(I): 15.2
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.229 / % possible all: 69.5

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: rigid body refinement of 1U1V
Starting model: 1U1V

1u1v


Resolution: 1.3→19.1 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.006 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15973 3287 5.1 %RANDOM
Rwork0.13344 ---
obs0.13482 61287 91.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.128 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 5 359 2573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0212274
X-RAY DIFFRACTIONr_bond_other_d00.022091
X-RAY DIFFRACTIONr_angle_refined_deg2.7141.9483111
X-RAY DIFFRACTIONr_angle_other_deg3.93834838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175300
X-RAY DIFFRACTIONr_chiral_restr0.1770.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0270.022644
X-RAY DIFFRACTIONr_gen_planes_other0.0690.02482
X-RAY DIFFRACTIONr_nbd_refined0.2420.2419
X-RAY DIFFRACTIONr_nbd_other0.2990.22371
X-RAY DIFFRACTIONr_nbtor_other0.120.21263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3850.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.240
X-RAY DIFFRACTIONr_mcbond_it2.6511.51453
X-RAY DIFFRACTIONr_mcangle_it3.58822348
X-RAY DIFFRACTIONr_scbond_it5.0953821
X-RAY DIFFRACTIONr_scangle_it7.4094.5763
X-RAY DIFFRACTIONr_rigid_bond_restr2.81622274
X-RAY DIFFRACTIONr_sphericity_free10.9692359
X-RAY DIFFRACTIONr_sphericity_bonded6.6722214
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 157
Rwork0.183 2943
Refinement TLS params.Method: refined / Origin x: 18.3438 Å / Origin y: 22.1671 Å / Origin z: 16.2598 Å
111213212223313233
T0.0028 Å2-0.0025 Å2-0.0022 Å2-0.0046 Å20.0021 Å2--0.003 Å2
L-0.0153 °2-0.0424 °20.0073 °2-0.1378 °2-0.0654 °2--0.041 °2
S-0.0016 Å °-0.0032 Å °-0.0007 Å °-0.0102 Å °0.0063 Å °0.0085 Å °0.0037 Å °-0.0055 Å °-0.0047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 27821 - 298
2X-RAY DIFFRACTION1AB10011

+
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