[English] 日本語
Yorodumi
- PDB-2ip2: Structure of the Pyocyanin Biosynthetic Protein PhzM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ip2
TitleStructure of the Pyocyanin Biosynthetic Protein PhzM
ComponentsProbable phenazine-specific methyltransferase
KeywordsTRANSFERASE / methyltransferase / phenazine / pyocyanin / phenazine-1-carboxylic acid / phzM
Function / homology
Function and homology information


phenazine-1-carboxylate N-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation
Similarity search - Function
Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phenazine-1-carboxylate N-methyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsLadner, J.E. / Parsons, J.F. / Robinson, H. / Shi, K.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and functional analysis of the pyocyanin biosynthetic protein PhzM from Pseudomonas aeruginosa.
Authors: Parsons, J.F. / Greenhagen, B.T. / Shi, K. / Calabrese, K. / Robinson, H. / Ladner, J.E.
History
DepositionOct 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable phenazine-specific methyltransferase
B: Probable phenazine-specific methyltransferase


Theoretical massNumber of molelcules
Total (without water)72,7952
Polymers72,7952
Non-polymers00
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-55 kcal/mol
Surface area27190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.970, 62.410, 68.750
Angle α, β, γ (deg.)97.47, 105.37, 108.09
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Probable phenazine-specific methyltransferase / Pyocyanin Biosynthetic Protein


Mass: 36397.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: phzM / Plasmid: PET28A / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HWH2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The well solution contained 18-21% PEG 3350, 0.1M magnesium chloride, 0.1M MOPS, pH 7.0. The drops were formed by mixing equal volumes of protein (13.5 mg/ml) and well solution, VAPOR ...Details: The well solution contained 18-21% PEG 3350, 0.1M magnesium chloride, 0.1M MOPS, pH 7.0. The drops were formed by mixing equal volumes of protein (13.5 mg/ml) and well solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 4, 2006 / Details: Blue Max-flux confocal
RadiationMonochromator: Blue Max-flux confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.8→29.4 Å / Num. all: 60747 / Num. obs: 60747 / % possible obs: 94.2 % / Redundancy: 7.36 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.31 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5841 / % possible all: 90.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
d*TREKdata reduction
d*TREKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.312 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24739 3079 5.1 %RANDOM
Rwork0.19354 ---
obs0.1963 57471 93.94 %-
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: 32.601 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0.74 Å2-1.1 Å2
2--0.08 Å2-0.23 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 0 512 5552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9737135
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0922.51251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.57215919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2491565
X-RAY DIFFRACTIONr_chiral_restr0.1330.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023981
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.22697
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23694
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2418
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3421.53392
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91425291
X-RAY DIFFRACTIONr_scbond_it3.00432091
X-RAY DIFFRACTIONr_scangle_it4.4584.51844
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.897 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.38 401 -
Rwork0.296 8073 -
obs--90.84 %

+
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