[English] 日本語
Yorodumi
- PDB-8q03: Metagenomic lipase ORF30 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q03
TitleMetagenomic lipase ORF30
Components(ORF30) x 2
KeywordsHYDROLASE / lipase / esterase / metagenomic / enzyme
Function / homologybutanoic acid
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsRangel Pereira, M. / Balan, A. / Hyvonen, M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: To Be Published
Title: Lipases isolated from metagenomic libraries
Authors: Rangel Pereira, M. / Balan, A. / Hyvonen, M.
History
DepositionJul 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORF30
B: ORF30
C: ORF30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,85122
Polymers107,0613
Non-polymers1,78919
Water19,7261095
1
A: ORF30
B: ORF30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,17213
Polymers72,1402
Non-polymers1,03311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-73 kcal/mol
Surface area24310 Å2
2
C: ORF30
hetero molecules

C: ORF30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,35618
Polymers69,8432
Non-polymers1,51316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5070 Å2
ΔGint-130 kcal/mol
Surface area24020 Å2
Unit cell
Length a, b, c (Å)182.376, 45.742, 135.369
Angle α, β, γ (deg.)90.000, 105.630, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-240-

ARG

21C-765-

HOH

-
Components

-
Protein , 2 types, 3 molecules ABC

#1: Protein ORF30


Mass: 36069.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Plasmid: pHAT2 / Production host: Escherichia coli (E. coli)
#2: Protein ORF30


Mass: 34921.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Plasmid: pHAT2 / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 1114 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1095 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6 M ammonium sulfate, 0.1 M Bicine, pH 9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.48→46.67 Å / Num. obs: 159190 / % possible obs: 88.3 % / Redundancy: 15 % / Biso Wilson estimate: 20.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.082 / Net I/σ(I): 11.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.48-1.570.9681.2151440.5711.1731
1.57-1.680.611209000.760.7181
1.68-1.810.348248960.9140.3971
1.81-1.980.189233590.9710.2151
1.98-2.220.109211770.9880.1241
2.22-2.560.076187510.9930.0871
2.56-3.130.059158780.9950.0681
3.13-4.420.049123660.9960.0561
4.42-46.670.04167190.9970.0481

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→46.67 Å / SU ML: 0.1693 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1798 8017 5.04 %
Rwork0.1439 151138 -
obs0.1457 159155 88.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.58 Å2
Refinement stepCycle: LAST / Resolution: 1.48→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7285 0 101 1095 8481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00567686
X-RAY DIFFRACTIONf_angle_d0.713910448
X-RAY DIFFRACTIONf_chiral_restr0.07621082
X-RAY DIFFRACTIONf_plane_restr0.00671409
X-RAY DIFFRACTIONf_dihedral_angle_d11.76572810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.39821490.38162348X-RAY DIFFRACTION42.25
1.5-1.510.34331550.29472797X-RAY DIFFRACTION49.51
1.51-1.530.30281560.25413009X-RAY DIFFRACTION53.18
1.53-1.550.27361730.23733304X-RAY DIFFRACTION58.36
1.55-1.570.27641720.21493635X-RAY DIFFRACTION63.37
1.57-1.590.30722090.20843831X-RAY DIFFRACTION68.29
1.59-1.620.24442280.19694133X-RAY DIFFRACTION73.37
1.62-1.640.24552490.1924480X-RAY DIFFRACTION79.23
1.64-1.670.24032490.18624758X-RAY DIFFRACTION84.56
1.67-1.690.22152390.18365160X-RAY DIFFRACTION89.79
1.69-1.720.27252940.20185482X-RAY DIFFRACTION97.37
1.72-1.750.23432810.17835715X-RAY DIFFRACTION100
1.75-1.790.21492910.1575631X-RAY DIFFRACTION99.97
1.79-1.830.21263130.14665694X-RAY DIFFRACTION100
1.83-1.860.20372980.13285612X-RAY DIFFRACTION100
1.86-1.910.17962750.13375786X-RAY DIFFRACTION100
1.91-1.960.18572980.13645635X-RAY DIFFRACTION99.97
1.96-2.010.17083170.13675664X-RAY DIFFRACTION99.95
2.01-2.070.18963360.13375672X-RAY DIFFRACTION99.95
2.07-2.130.18112940.13785661X-RAY DIFFRACTION99.95
2.13-2.210.16833020.13425693X-RAY DIFFRACTION99.98
2.21-2.30.18143340.12515694X-RAY DIFFRACTION99.92
2.3-2.40.16052910.12965709X-RAY DIFFRACTION99.97
2.4-2.530.17313060.13865718X-RAY DIFFRACTION99.98
2.53-2.690.18322970.14455708X-RAY DIFFRACTION99.92
2.69-2.90.17772950.14945680X-RAY DIFFRACTION99.93
2.9-3.190.17792920.1475776X-RAY DIFFRACTION99.87
3.19-3.650.14763130.13375751X-RAY DIFFRACTION99.8
3.65-4.60.15483170.11985778X-RAY DIFFRACTION99.53
4.6-46.670.16822940.15225624X-RAY DIFFRACTION94.06

+
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