[English] 日本語
Yorodumi
- PDB-3bvq: Crystal Structure of Apo NotI Restriction Endonuclease -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bvq
TitleCrystal Structure of Apo NotI Restriction Endonuclease
ComponentsNotI restriction endonuclease
KeywordsHYDROLASE / Restriction enzyme fold / PD-(D/E)-XK / Restriction endonuclease / rare-cutting / Fe-Cys4 motif / iron-sulfur protein
Function / homologyendonuclease activity / identical protein binding / metal ion binding / : / NotI restriction endonuclease
Function and homology information
Biological speciesNocardia otitidiscaviarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLambert, A.R. / Sussman, D. / Shen, B. / Stoddard, B.L.
CitationJournal: Structure / Year: 2008
Title: Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.
Authors: Lambert, A.R. / Sussman, D. / Shen, B. / Maunus, R. / Nix, J. / Samuelson, J. / Xu, S.Y. / Stoddard, B.L.
History
DepositionJan 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: NotI restriction endonuclease
B: NotI restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8106
Polymers85,5072
Non-polymers3044
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.893, 74.893, 274.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROAA12 - 36412 - 364
2THRTHRBB12 - 36612 - 366

-
Components

#1: Protein NotI restriction endonuclease


Mass: 42753.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia otitidiscaviarum (bacteria) / Gene: notIR / Production host: Escherichia coli (E. coli) / References: UniProt: Q2I6W2
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.27 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9804, 0.9805, 0.9744, 1.0048
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98041
20.98051
30.97441
41.00481
ReflectionResolution: 2.8→50 Å / Num. obs: 20201 / % possible obs: 99.6 % / Redundancy: 26 % / Rmerge(I) obs: 0.109 / Χ2: 0.984 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 21 % / Rmerge(I) obs: 0.317 / Num. unique all: 1907 / Χ2: 0.952 / % possible all: 97.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
SHARPphasing
RefinementResolution: 2.8→45.83 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.841 / SU B: 54.807 / SU ML: 0.486 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.335 1028 5.1 %RANDOM
Rwork0.262 ---
obs0.266 20107 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.375 Å2
Baniso -1Baniso -2Baniso -3
1--5.6 Å20 Å20 Å2
2---5.6 Å20 Å2
3---11.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 12 0 5160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225303
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9417252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0545689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04523.657216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77915717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2731527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024117
X-RAY DIFFRACTIONr_nbd_refined0.1970.22398
X-RAY DIFFRACTIONr_nbtor_refined0.30.23615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.26
X-RAY DIFFRACTIONr_mcbond_it0.3061.53515
X-RAY DIFFRACTIONr_mcangle_it0.50925503
X-RAY DIFFRACTIONr_scbond_it0.44532028
X-RAY DIFFRACTIONr_scangle_it0.7164.51749
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2311 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.480.5
MEDIUM THERMAL0.172
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 67 -
Rwork0.367 1332 -
all-1399 -
obs--96.15 %
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)
11.4421-0.59-0.42840.54270.14390.71640.0449-0.052-0.6187-0.0147-0.0240.14660.16730.0047-0.0209-0.1187-0.0587-0.0180.0466-0.01930.179744.878555.6957111.9606
21.33180.1173-0.51371.10830.20450.2550.0059-0.05610.08120.1510.020.06680.02730.0013-0.026-0.13920.01380.01320.04930.0125-0.070527.410280.3579124.6286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 36412 - 364
2X-RAY DIFFRACTION2BB12 - 36612 - 366

+
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