[English] 日本語
Yorodumi
- PDB-4e3y: X-ray structure of the Serratia marcescens endonuclease at 0.95 A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e3y
TitleX-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution
ComponentsNuclease
KeywordsHYDROLASE / Rossmann Fold / Nucleic Acid / Extracellular
Function / homology
Function and homology information


Serratia marcescens nuclease / endonuclease activity / nucleic acid binding / extracellular region / metal ion binding
Similarity search - Function
DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease ...DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Nuclease
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.95 Å
AuthorsLashkov, A.A. / Balaev, V.V. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
CitationJournal: To be Published
Title: X-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution
Authors: Lashkov, A.A. / Balaev, V.V. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionMar 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Nuclease
B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,04110
Polymers53,4782
Non-polymers5638
Water12,340685
1
A: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9314
Polymers26,7391
Non-polymers1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1096
Polymers26,7391
Non-polymers3715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.265, 73.418, 67.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Nuclease / / Endonuclease / Nuclease isoform Sm2 / Nuclease isoform Sm3 / Nuclease isoform Sm1


Mass: 26738.896 Da / Num. of mol.: 2 / Fragment: UNP residues 22-266 / Source method: isolated from a natural source / Source: (natural) Serratia marcescens (bacteria) / Strain: SM6 / References: UniProt: P13717, Serratia marcescens nuclease

-
Non-polymers , 6 types, 693 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 2.54 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 10 mM TRIS-HCl, 1 mM Mg(2+), PEG4000, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.847 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 27, 2011
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.847 Å / Relative weight: 1
ReflectionResolution: 0.949772→27.5967 Å / Num. all: 332540 / Num. obs: 313007 / % possible obs: 94.1264 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8T

1g8t


Resolution: 0.95→8 Å / Occupancy max: 1 / Occupancy min: 0.07 / FOM work R set: 0.929 / SU ML: 0.06 / σ(F): 2 / Phase error: 13.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1453 15589 5.04 %Random
Rwork0.1302 ---
obs0.1309 309541 93.26 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.595 Å2 / ksol: 0.492 e/Å3
Displacement parametersBiso max: 48.48 Å2 / Biso mean: 12.1759 Å2 / Biso min: 3.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.8343 Å20 Å2-0 Å2
2--2.2791 Å2-0 Å2
3----1.4448 Å2
Refinement stepCycle: LAST / Resolution: 0.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 33 685 4402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174010
X-RAY DIFFRACTIONf_angle_d1.825487
X-RAY DIFFRACTIONf_chiral_restr0.117605
X-RAY DIFFRACTIONf_plane_restr0.012719
X-RAY DIFFRACTIONf_dihedral_angle_d11.2261512
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.9498-0.96050.27664750.27138695917084
0.9605-0.97180.28454700.26429439990990
0.9718-0.98370.27744610.24659496995791
0.9837-0.99610.23984940.23339492998691
0.9961-1.00920.22644980.21659489998791
1.0092-1.0230.21345110.196395351004692
1.023-1.03760.19615410.186395361007792
1.0376-1.0530.19275040.171996721017692
1.053-1.06940.16874900.157996751016593
1.0694-1.08690.16045110.144297731028493
1.0869-1.10560.14295300.133196921022293
1.1056-1.12570.12974780.122298671034594
1.1257-1.14730.13435580.115898611041994
1.1473-1.17060.12864990.1199641046395
1.1706-1.1960.11775330.104199641049795
1.196-1.22370.12035240.1081100271055196
1.2237-1.25420.13135450.103799791052496
1.2542-1.2880.11775610.0995100101057196
1.288-1.32570.10895520.0986100131056596
1.3257-1.36830.11375380.0907100021054095
1.3683-1.41690.1165250.0935100101053595
1.4169-1.47330.11085180.0896100021052095
1.4733-1.53990.11415330.089999201045394
1.5399-1.62050.10685330.089398671040094
1.6205-1.72110.11275410.095298101035193
1.7211-1.85240.13055310.114498461037793
1.8524-2.03610.14165630.1232100921065595
2.0361-2.32430.13225380.1222100981063695
2.3243-2.90490.14845240.1331100651058994
2.9049-8.00020.16965100.1563100611057191

+
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