[English] 日本語
Yorodumi
- PDB-3qpa: Structure of Fusarium Solani Cutinase expressed in Pichia pastoris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qpa
TitleStructure of Fusarium Solani Cutinase expressed in Pichia pastoris
ComponentsCutinase
KeywordsHYDROLASE / alpha-beta hydrolase fold / esterase / cutin / mono-ethyl phosphorylated serine residue / secreted
Function / homology
Function and homology information


cutinase / cutinase activity / carbohydrate catabolic process / extracellular region
Similarity search - Function
Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cutinase / Cutinase 1
Similarity search - Component
Biological speciesNectria haematococca (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsLu, A. / Gosser, Y. / Montclare, J.K. / Liu, Z. / Kong, X.
CitationJournal: To be Published
Title: Structure of Fusarium Solani Cutinase expressed in Pichia pastoris
Authors: Lu, A. / Gosser, Y. / Montclare, J.K. / Liu, Z. / Kong, X.
History
DepositionFeb 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,5791
Polymers20,5791
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.006, 66.165, 36.755
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cutinase / Cutin hydrolase 1


Mass: 20579.004 Da / Num. of mol.: 1 / Fragment: unp residues 32-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nectria haematococca (fungus) / Strain: 77-13-4 / FGSC 9596 / MPVI / Gene: CUT1, CUTA, NECHADRAFT_81019 / Production host: Pichia pastoris (fungus) / References: UniProt: C7ZGJ1, UniProt: P00590*PLUS, cutinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% (w/v) PEG6000, 0.1M citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.77009 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 5, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77009 Å / Relative weight: 1
ReflectionResolution: 0.85→13.69 Å / Num. all: 141550 / Num. obs: 141550 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 0.8503→0.8599 Å / % possible all: 93

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1CEX

1cex


Resolution: 0.85→13.69 Å / SU ML: 0.08 / σ(F): 1.34 / σ(I): 0 / Phase error: 7.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1169 7113 5.03 %Random
Rwork0.1097 ---
all0.1241 141550 --
obs0.1101 141550 96.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.158 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5251 Å2-0 Å20.2709 Å2
2---0.6544 Å2-0 Å2
3---0.1293 Å2
Refinement stepCycle: LAST / Resolution: 0.85→13.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 327 1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011572
X-RAY DIFFRACTIONf_angle_d1.4992155
X-RAY DIFFRACTIONf_dihedral_angle_d11.642607
X-RAY DIFFRACTIONf_chiral_restr0.087244
X-RAY DIFFRACTIONf_plane_restr0.009291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8503-0.85990.12312290.1224294X-RAY DIFFRACTION93
0.8599-0.870.13282310.11564344X-RAY DIFFRACTION95
0.87-0.88070.13672300.11534414X-RAY DIFFRACTION95
0.8807-0.89180.12192190.10534397X-RAY DIFFRACTION95
0.8918-0.90350.11912340.10184374X-RAY DIFFRACTION95
0.9035-0.91590.10422410.09814387X-RAY DIFFRACTION96
0.9159-0.9290.10662250.09224406X-RAY DIFFRACTION96
0.929-0.94290.10612420.08894474X-RAY DIFFRACTION96
0.9429-0.95760.08932430.08654391X-RAY DIFFRACTION96
0.9576-0.97330.09552170.08484511X-RAY DIFFRACTION96
0.9733-0.99010.08622460.084411X-RAY DIFFRACTION97
0.9901-1.00810.08612490.07914467X-RAY DIFFRACTION97
1.0081-1.02740.10442500.07844490X-RAY DIFFRACTION97
1.0274-1.04840.09072340.07834460X-RAY DIFFRACTION97
1.0484-1.07120.07762530.0764486X-RAY DIFFRACTION97
1.0712-1.09610.08022510.0734494X-RAY DIFFRACTION98
1.0961-1.12350.07732160.07164526X-RAY DIFFRACTION98
1.1235-1.15390.08212670.07024470X-RAY DIFFRACTION98
1.1539-1.18780.08062630.07194546X-RAY DIFFRACTION98
1.1878-1.22610.08472240.07774576X-RAY DIFFRACTION98
1.2261-1.26990.08732510.08154543X-RAY DIFFRACTION99
1.2699-1.32070.0982430.08454567X-RAY DIFFRACTION99
1.3207-1.38080.09512160.09224585X-RAY DIFFRACTION99
1.3808-1.45350.11492170.09894659X-RAY DIFFRACTION99
1.4535-1.54440.10392040.09954616X-RAY DIFFRACTION99
1.5444-1.66350.11362640.10254608X-RAY DIFFRACTION100
1.6635-1.83050.11462270.11264635X-RAY DIFFRACTION100
1.8305-2.09460.12642480.1234596X-RAY DIFFRACTION99
2.0946-2.63590.12332670.12984554X-RAY DIFFRACTION98
2.6359-13.69220.17022120.17244156X-RAY DIFFRACTION88

+
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