[English] 日本語
Yorodumi
- PDB-4q3k: Crystal structure of MGS-M1, an alpha/beta hydrolase enzyme from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q3k
TitleCrystal structure of MGS-M1, an alpha/beta hydrolase enzyme from a Medee basin deep-sea metagenome library
ComponentsMGS-M1
KeywordsHYDROLASE / metagenome / metagenomic library / alpha and beta proteins / alpha/beta hydrolase superfamily / esterase/lipase fold
Function / homology
Function and homology information


serine-type peptidase activity
Similarity search - Function
Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLUORIDE ION / TRIETHYLENE GLYCOL / Esterase lipase-like protein
Similarity search - Component
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsStogios, P.J. / Xu, X. / Cui, H. / Alcaide, M. / Ferrer, M. / Savchenko, A.
CitationJournal: Environ Microbiol / Year: 2015
Title: Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats.
Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / ...Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / Jebbar, M. / Jaeger, K.E. / Yakimov, M.M. / Yakunin, A.F. / Golyshin, P.N. / Golyshina, O.V. / Savchenko, A. / Ferrer, M.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Sep 20, 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: MGS-M1
B: MGS-M1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0889
Polymers58,5292
Non-polymers5597
Water11,926662
1
A: MGS-M1
B: MGS-M1
hetero molecules

A: MGS-M1
B: MGS-M1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,17618
Polymers117,0574
Non-polymers1,11914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13440 Å2
ΔGint-65 kcal/mol
Surface area34960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.991, 82.716, 77.377
Angle α, β, γ (deg.)90.00, 109.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-486-

HOH

31A-717-

HOH

41B-598-

HOH

DetailsTHE AUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN AT THIS TIME

-
Components

#1: Protein MGS-M1


Mass: 29264.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: p15-TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A0A0B5KGV8*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O
Source detailsTHE SAMPLE WAS EXTRACTED FROM MEDEE BASIN DEEP-SEA AND ANALYZED BY USING METAGENOME LIBRARY TECHNIQUE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% potassium fluoride, 20% PEG3350. cryoprotectant:12% glycerol., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 17, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→30 Å / Num. obs: 63876 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.19
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.09 / % possible all: 83

-
Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: dev_1538)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HXK

3hxk


Resolution: 1.57→28.296 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 1869 3.11 %
Rwork0.1463 --
obs0.1476 63864 83.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→28.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3819 0 34 662 4515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094062
X-RAY DIFFRACTIONf_angle_d1.235534
X-RAY DIFFRACTIONf_dihedral_angle_d13.1691528
X-RAY DIFFRACTIONf_chiral_restr0.053612
X-RAY DIFFRACTIONf_plane_restr0.006715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5693-1.59170.3281010.29663080X-RAY DIFFRACTION58
1.5917-1.61550.31941180.29683553X-RAY DIFFRACTION69
1.6155-1.64070.31861290.28923924X-RAY DIFFRACTION74
1.6407-1.66760.31681260.29444019X-RAY DIFFRACTION78
1.6676-1.69640.3171290.27934166X-RAY DIFFRACTION80
1.6964-1.72720.29561320.24074236X-RAY DIFFRACTION81
1.7272-1.76040.27581310.22824155X-RAY DIFFRACTION80
1.7604-1.79640.26711340.2174308X-RAY DIFFRACTION81
1.7964-1.83540.30961400.19344278X-RAY DIFFRACTION82
1.8354-1.87810.2411380.18624291X-RAY DIFFRACTION83
1.8781-1.92510.21321440.17394370X-RAY DIFFRACTION83
1.9251-1.97710.20021400.16714385X-RAY DIFFRACTION84
1.9771-2.03530.20841440.16064387X-RAY DIFFRACTION85
2.0353-2.10090.19051410.14374406X-RAY DIFFRACTION85
2.1009-2.1760.21391420.13544466X-RAY DIFFRACTION85
2.176-2.26310.16071480.13264510X-RAY DIFFRACTION87
2.2631-2.3660.18821510.12944594X-RAY DIFFRACTION87
2.366-2.49070.17691370.13864590X-RAY DIFFRACTION88
2.4907-2.64670.19741500.14044601X-RAY DIFFRACTION89
2.6467-2.85080.18651470.14184722X-RAY DIFFRACTION90
2.8508-3.13740.14751570.13884722X-RAY DIFFRACTION91
3.1374-3.59060.18241510.12184739X-RAY DIFFRACTION91
3.5906-4.52080.13211550.10814776X-RAY DIFFRACTION92
4.5208-28.3010.14981560.12584907X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.795-0.1210.89611.0182-0.4583.3241-0.03670.03380.12860.0255-0.011-0.0094-0.1490.31430.05680.1183-0.01050.00150.1399-0.02130.130823.698596.92412.8916
22.25770.31030.11811.0016-0.21731.9502-0.0034-0.32650.08660.04560.0225-0.0115-0.01010.0786-0.02090.13780.0078-0.00390.1749-0.03490.128519.183599.046525.0075
32.3878-0.03070.38641.03970.07761.75020.0244-0.2479-0.12510.0782-0.01010.00450.061-0.0711-0.0070.1119-0.00570.00240.13780.02490.13725.876993.255919.4398
41.42380.5276-0.91971.0432-0.80712.45450.00690.0365-0.0811-0.0133-0.0594-0.06390.03030.31490.06050.11870.0115-0.00260.1635-0.02080.131326.347992.793-5.5306
52.735-0.61540.05070.92940.07231.81520.06230.4131-0.132-0.0842-0.1011-0.01810.06820.31170.04980.14670.02070.00510.2426-0.04140.14725.182990.5466-18.2744
62.31550.14850.30761.25740.18311.69630.03940.28080.036-0.0708-0.0369-0.0077-0.0510.1012-0.010.10750.0036-0.00180.17520.00570.118910.920496.8711-16.8415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi -1:74
2X-RAY DIFFRACTION2chain A and resi 75:145
3X-RAY DIFFRACTION3chain A and resi 146:239
4X-RAY DIFFRACTION4chain B and resi -1:74
5X-RAY DIFFRACTION5chain B and resi 75:145
6X-RAY DIFFRACTION6chain B and resi 146:239

+
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