[English] 日本語
Yorodumi
- PDB-2h9c: Native Crystal Structure of the Isochorismate-Pyruvate Lyase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h9c
TitleNative Crystal Structure of the Isochorismate-Pyruvate Lyase from Pseudomonas aeruginosa
ComponentsSalicylate biosynthesis protein pchBIsochorismate lyase
KeywordsLYASE / intertwinded dimer
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 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
NITRATE ION / Isochorismate pyruvate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLamb, A.L. / Zaitseva, J. / Lu, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Two Crystal Structures of the Isochorismate Pyruvate Lyase from Pseudomonas aeruginosa.
Authors: Zaitseva, J. / Lu, J. / Olechoski, K.L. / Lamb, A.L.
History
DepositionJun 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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

-
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)22,9207
Polymers22,6102
Non-polymers3105
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-29 kcal/mol
Surface area9550 Å2
MethodPISA
2
A: Salicylate biosynthesis protein pchB
B: Salicylate biosynthesis protein pchB
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,84014
Polymers45,2204
Non-polymers62010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13700 Å2
ΔGint-86 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.148, 93.148, 60.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe asymmetric unit contains one dimer, which is the biological asssembly.

-
Components

#1: Protein Salicylate biosynthesis protein pchB / Isochorismate lyase / Isochorismate-Pyruvate Lyase


Mass: 11304.909 Da / Num. of mol.: 2 / Fragment: residues 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PchB / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q51507, Lyases; Carbon-carbon lyases; Other carbon-carbon lyases
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.1 M acetate buffer, 4.8 - 5.3 M ammonium nitrate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 138 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2004
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 9.2 % / Av σ(I) over netI: 12.6 / Number: 106446 / Rmerge(I) obs: 0.067 / Χ2: 0.94 / D res high: 2.35 Å / D res low: 100 Å / Num. obs: 11526 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.061009910.0330.88.6
4.025.0699.910.0410.9059.3
3.514.0210010.0490.9849.3
3.193.5199.910.0691.0169.4
2.963.1910010.1020.9879.4
2.792.9610010.1390.9839.4
2.652.7999.910.1790.9379.4
2.532.6510010.2380.9569.3
2.432.5310010.3070.9359.2
2.352.4310010.3780.9139
ReflectionResolution: 2.35→28.9 Å / Num. obs: 11526 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.942 / Net I/σ(I): 12.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 9 % / Rmerge(I) obs: 0.378 / Num. unique all: 1120 / Χ2: 0.913 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ECM

1ecm


Resolution: 2.35→28.9 Å / FOM work R set: 0.806 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1162 10.1 %random
Rwork0.224 ---
obs0.224 11246 97.7 %-
all-11515 --
Solvent computationBsol: 44.597 Å2
Displacement parametersBiso mean: 42.792 Å2
Baniso -1Baniso -2Baniso -3
1-2.488 Å20 Å20 Å2
2--2.488 Å20 Å2
3----4.977 Å2
Refinement stepCycle: LAST / Resolution: 2.35→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 20 55 1472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4511.5
X-RAY DIFFRACTIONc_scbond_it2.1662
X-RAY DIFFRACTIONc_mcangle_it2.4022
X-RAY DIFFRACTIONc_scangle_it3.3132.5
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.08
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.35-2.390.29570.246393450
2.39-2.420.353500.238410460
2.42-2.460.354500.249422472
2.46-2.50.232390.241430469
2.5-2.550.315500.22412462
2.55-2.60.322580.252413471
2.6-2.650.353430.246439482
2.65-2.710.256600.23406466
2.71-2.770.324450.238440485
2.77-2.840.276560.231427483
2.84-2.920.382580.238436494
2.92-30.335430.244456499
3-3.10.275530.229415468
3.1-3.210.232410.242450491
3.21-3.340.379480.247449497
3.34-3.490.218510.216435486
3.49-3.680.212450.195445490
3.68-3.910.232420.185460502
3.91-4.210.204440.179461505
4.21-4.630.263450.188468513
4.63-5.30.23600.199453513
5.3-6.680.357640.304465529
6.68-1000.229600.251499559
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3nitrate.param

+
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