[English] 日本語
Yorodumi
- PDB-3rem: Structure of the Isochorismate-Pyruvate Lyase from Pseudomonas ae... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rem
TitleStructure of the Isochorismate-Pyruvate Lyase from Pseudomonas aerugionsa with Bound Salicylate and Pyruvate
ComponentsSalicylate biosynthesis protein pchBIsochorismate lyase
KeywordsLYASE / INTERTWINED DIMER / Mutase
Function / homology
Function and homology information


pyochelin biosynthetic process / isochorismate lyase / isochorismate pyruvate lyase activity / carbon-oxygen lyase activity / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity
Similarity search - Function
Salicylate biosynthesis protein PchB / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PYRUVIC ACID / 2-HYDROXYBENZOIC ACID / Isochorismate pyruvate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOlucha, J. / Ouellette, A.N. / Luo, Q. / Lamb, A.L.
CitationJournal: Biochemistry / Year: 2011
Title: pH Dependence of Catalysis by Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase: Implications for Transition State Stabilization and the Role of Lysine 42.
Authors: Olucha, J. / Ouellette, A.N. / Luo, Q. / Lamb, A.L.
History
DepositionApr 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Salicylate biosynthesis protein pchB
B: Salicylate biosynthesis protein pchB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3466
Polymers22,8942
Non-polymers4524
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-18 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.316, 60.254, 60.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Salicylate biosynthesis protein pchB / Isochorismate lyase


Mass: 11447.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4230, pchB / Plasmid: PET29B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q51507, Lyases; Carbon-carbon lyases; Other carbon-carbon lyases
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate, 6% glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 30, 2010 / Details: Rh coated flat mirror, toroidal focusing mirror
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→31.71 Å / Num. all: 13010 / Num. obs: 12438 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.058 / Net I/σ(I): 15.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 1816 / Rsym value: 0.226 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0072 & PHENIX 1.7-650refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H9D

2h9d


Resolution: 1.95→31.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.498 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.23
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29084 1235 10 %RANDOM
Rwork0.23086 ---
all0.23665 12438 --
obs0.23665 11177 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.308 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 32 44 1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221635
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9662213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6695194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.59122.68382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67915273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7311520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211286
X-RAY DIFFRACTIONr_mcbond_it0.5461.5976
X-RAY DIFFRACTIONr_mcangle_it1.03821563
X-RAY DIFFRACTIONr_scbond_it1.8373659
X-RAY DIFFRACTIONr_scangle_it3.0944.5650
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 115 -
Rwork0.264 801 -
obs--96.83 %

+
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