[English] 日本語
Yorodumi
- PDB-3cn9: Crystal Structure Analysis of the Carboxylesterase PA3859 from Ps... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cn9
TitleCrystal Structure Analysis of the Carboxylesterase PA3859 from Pseudomonas aeruginosa PAO1- orthorhombic crystal form
ComponentsCarboxylesterase
KeywordsHYDROLASE / alpha/beta hydrolase fold super-family
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLamba, D. / Pesaresi, A.
Citation
Journal: Biochimie / Year: 2010
Title: Insights into the fatty acid chain length specificity of the carboxylesterase PA3859 from Pseudomonas aeruginosa: A combined structural, biochemical and computational study.
Authors: Pesaresi, A. / Lamba, D.
#1: Journal: CURR.MICROBIOL. / Year: 2005
Title: Isolation, Characterization, and Heterologous Expression of a Carboxylesterase of Pseudomonas aeruginosa PAO1
Authors: Pesaresi, A. / Devescovi, G. / Lamba, D. / Venturi, V. / Degrassi, G.
#2: Journal: BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS / Year: 2005
Title: Crystallization, X-ray Diffraction Analysis and Phasing of Carboxylesterase PA3859 from Pseudomonas aeruginosa
Authors: Pesaresi, A. / Lamba, D.
History
DepositionMar 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carboxylesterase
B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3895
Polymers49,4402
Non-polymers9493
Water5,386299
1
A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2553
Polymers24,7201
Non-polymers5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1342
Polymers24,7201
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.423, 96.363, 68.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Carboxylesterase


Mass: 24719.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3859 / Plasmid: pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (pREP4) / References: UniProt: Q9HXE7, carboxylesterase
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 200mM AMS, 100 mM MES, 30% w/v PEG-MME 5000, squared bipyramids appeared within 7 to 10 days, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.278
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2002 / Details: THREE-SEGMENT PT-COATED TOROIDAL MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 2.09→29.05 Å / Num. obs: 36106 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.06 / Net I/σ(I): 6.4
Reflection shellResolution: 2.09→2.1 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / Rsym value: 0.39 / % possible all: 90.5

-
Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AUO, CHAIN A

1auo


Resolution: 2.09→29.05 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1173999.84 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3602 10 %RANDOM
Rwork0.196 ---
obs0.196 36106 95.5 %-
all-36512 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.92 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--1.88 Å20 Å2
3----2.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.09→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 64 299 3655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.4221.5
X-RAY DIFFRACTIONc_mcangle_it3.0862
X-RAY DIFFRACTIONc_scbond_it4.0512
X-RAY DIFFRACTIONc_scangle_it5.2752.5
LS refinement shellResolution: 2.09→2.22 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 526 10.1 %
Rwork0.222 4686 -
obs--83.3 %

+
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