[English] 日本語
Yorodumi
- PDB-3hgw: Apo Structure of Pseudomonas aeruginosa Isochorismate-Pyruvate Ly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hgw
TitleApo Structure of Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase I87T mutant
ComponentsSalicylate biosynthesis protein pchB
KeywordsLYASE / siderophore biosynthesis / pyochelin / isochorismate-pyruvate lyase / chorismate mutase / PchB
Function / homology
Function and homology information


pyochelin biosynthetic process / isochorismate lyase / carbon-oxygen lyase activity / isochorismate pyruvate 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, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Salicylate biosynthesis protein PchB / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Isochorismate pyruvate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLuo, Q. / Lamb, A.L.
CitationJournal: Biochemistry / Year: 2009
Title: Structure-function analyses of isochorismate-pyruvate lyase from Pseudomonas aeruginosa suggest differing catalytic mechanisms for the two pericyclic reactions of this bifunctional enzyme
Authors: Luo, Q. / Olucha, J. / Lamb, A.L.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 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
C: Salicylate biosynthesis protein pchB
D: Salicylate biosynthesis protein pchB
A: Salicylate biosynthesis protein pchB
B: Salicylate biosynthesis protein pchB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7805
Polymers45,7404
Non-polymers401
Water1,36976
1
C: Salicylate biosynthesis protein pchB
D: Salicylate biosynthesis protein pchB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9103
Polymers22,8702
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-35 kcal/mol
Surface area9740 Å2
MethodPISA
2
A: Salicylate biosynthesis protein pchB
B: Salicylate biosynthesis protein pchB


Theoretical massNumber of molelcules
Total (without water)22,8702
Polymers22,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-37 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.503, 74.919, 88.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Salicylate biosynthesis protein pchB


Mass: 11435.011 Da / Num. of mol.: 4 / Mutation: I87T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: pchB, PA4230 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q51507, Lyases; Carbon-carbon lyases; Other carbon-carbon lyases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-tris propane, pH 6.5, 0.14 M calcium chloride, 23% PEG 3350, and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

-
Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. obs: 17729 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Χ2: 0.884 / Net I/σ(I): 14.686
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.25-2.3370.35417260.86898.5
2.33-2.4270.2817360.77999.4
2.42-2.5370.24617450.85299.1
2.53-2.6770.20917450.86199.7
2.67-2.837.10.16417470.94399.5
2.83-3.0570.1417840.93999.7
3.05-3.3670.11117510.94699.9
3.36-3.8570.07618040.832100
3.85-4.8570.05718110.863100
4.85-1006.60.04518800.95997.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H9D

2h9d


Resolution: 2.25→23.21 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.908 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.241
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 900 5.1 %RANDOM
Rwork0.219 ---
obs0.221 17678 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.04 Å2 / Biso mean: 20.028 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.25→23.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 1 76 2799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222782
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9433761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6825329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77522.877146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04915473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8151533
X-RAY DIFFRACTIONr_chiral_restr0.0740.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022140
X-RAY DIFFRACTIONr_nbd_refined0.1830.21316
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.287
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0640.22
X-RAY DIFFRACTIONr_mcbond_it0.5551.51742
X-RAY DIFFRACTIONr_mcangle_it0.82422667
X-RAY DIFFRACTIONr_scbond_it1.29631234
X-RAY DIFFRACTIONr_scangle_it2.1374.51094
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 63 -
Rwork0.22 1217 -
all-1280 -
obs--98.99 %

+
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