[English] 日本語
Yorodumi
- PDB-2q10: RESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q10
TitleRESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE COMPLEX
Components
  • DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
  • DNA (5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3')
  • R.BcnI
KeywordsHYDROLASE/DNA / ENDONUCLEASE-DNA COMPLEX / RESTRICTION ENZYME / BCNI / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


MvaI/BcnI restriction endonuclease, catalytic domain / MvaI/BcnI restriction endonuclease, recognition domain / MvaI/BcnI restriction endonuclease, catalytic domain / MvaI/BcnI restriction endonuclease / MvaI/BcnI restriction endonuclease, recognition domain / MvaI/BcnI restriction endonuclease family / PvuII Endonuclease; Chain A / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / R.BcnI
Similarity search - Component
Biological speciesBrevibacillus centrosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, C. / Siksnys, V. / Bochtler, M.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA.
Authors: Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Szczepanowski, R.H. / Urbanke, C. / Siksnys, V. / Bochtler, M.
#1: Journal: To be Published
Title: Restriction Endonucleases that Resemble a Component of the Bacterial DNA Repair Machinery
Authors: Sokolowska, M. / Kaus-Drobek, M. / Czapinska, H. / Tamulaitis, G. / Siksnys, V. / Bochtler, M.
History
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_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
C: DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
D: DNA (5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3')
E: DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
F: DNA (5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3')
A: R.BcnI
B: R.BcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,27711
Polymers68,0866
Non-polymers1915
Water11,620645
1
C: DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
D: DNA (5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3')
A: R.BcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1596
Polymers34,0433
Non-polymers1163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')
F: DNA (5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3')
B: R.BcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1195
Polymers34,0433
Non-polymers762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.354, 87.551, 79.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
DNA chain , 2 types, 4 molecules CEDF

#1: DNA chain DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3')


Mass: 3352.214 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3')


Mass: 3356.182 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Protein , 1 types, 2 molecules AB

#3: Protein R.BcnI


Mass: 27334.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus centrosporus (bacteria) / Gene: bcnIR / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267 / References: UniProt: Q8RNV8

-
Non-polymers , 3 types, 650 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.02 M CALCIUM CHLORIDE DIHYDRATE, 0.1 M SODIUM ACETATE TRIHYDRATE, 30% (V/V) 2-METHYL-2,4-PENTANEDIOL , pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM CHLORIDE DIHYDRATE11
2SODIUM ACETATE TRIHYDRATE11
32-METHYL-2,4-PENTANEDIOL11
4CALCIUM CHLORIDE DIHYDRATE12
5SODIUM ACETATE TRIHYDRATE12
62-METHYL-2,4-PENTANEDIOL12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2006 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 57635 / Num. obs: 57635 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 5.8
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8336 / Rsym value: 0.26 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ODI

2odi


Resolution: 1.75→29.72 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.451 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS REFINEMENT HAVE BEEN USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2882 5 %RANDOM
Rwork0.174 ---
all0.176 57579 --
obs0.176 57579 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 890 5 645 5384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225175
X-RAY DIFFRACTIONr_bond_other_d0.0070.023330
X-RAY DIFFRACTIONr_angle_refined_deg1.352.1937173
X-RAY DIFFRACTIONr_angle_other_deg0.91138206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94924.66191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79615830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3471526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025094
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02898
X-RAY DIFFRACTIONr_nbd_refined0.1990.2891
X-RAY DIFFRACTIONr_nbd_other0.2090.23576
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22221
X-RAY DIFFRACTIONr_nbtor_other0.0790.22350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2531
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1510.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7991.52656
X-RAY DIFFRACTIONr_mcbond_other0.1661.51029
X-RAY DIFFRACTIONr_mcangle_it1.03224134
X-RAY DIFFRACTIONr_scbond_it1.833206
X-RAY DIFFRACTIONr_scangle_it2.2374.53039
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 204 -
Rwork0.229 4004 -
obs-4004 100 %
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)
10.8372-0.0446-0.17341.9141-0.20110.66010.02670.0260.02540.0653-0.01510.0062-0.101-0.0226-0.0116-0.04680.003-0.0039-0.0386-0.00240.00748.71826.39747.642
20.4679-0.2670.00910.53550.09730.8476-0.0528-0.06070.0377-0.01370.0236-0.1026-0.01990.24110.0292-0.0529-0.0084-0.0070.03810.01150.014469.92513.85949.636
31.2302-0.2925-0.17071.40130.14370.5426-0.0332-0.12150.05370.08280.05540.0268-0.0679-0.0458-0.0222-0.05240.0187-0.0093-0.0308-0.0033-0.00949.36225.77989.547
40.83760.010.18050.66250.07720.3235-0.0317-0.071-0.0101-0.00160.0276-0.1197-0.01940.03780.0041-0.0509-0.0035-0.0043-0.0468-0.00280.015470.46213.6688.97
51.28350.15270.20370.6858-0.01131.1066-0.00320.034-0.0035-0.04340.0819-0.01020.04790.0461-0.0787-0.04470.01040.0038-0.02-0.01380.006659.57712.11846.629
61.1242-0.13210.61450.4209-0.0821.17680.0061-0.004-0.0462-0.02220.07070.0035-0.0035-0.0209-0.0768-0.04290.00660.003-0.054-0.01460.015659.88611.95286.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE1 - 691 - 69
2X-RAY DIFFRACTION1AE156 - 182156 - 182
3X-RAY DIFFRACTION1AE233 - 238233 - 238
4X-RAY DIFFRACTION2AE70 - 15570 - 155
5X-RAY DIFFRACTION2AE183 - 232183 - 232
6X-RAY DIFFRACTION3BF1 - 691 - 69
7X-RAY DIFFRACTION3BF156 - 182156 - 182
8X-RAY DIFFRACTION3BF233 - 238233 - 238
9X-RAY DIFFRACTION4BF70 - 15570 - 155
10X-RAY DIFFRACTION4BF183 - 232183 - 232
11X-RAY DIFFRACTION5CA-4 - 61 - 11
12X-RAY DIFFRACTION5DB-4 - 61 - 11
13X-RAY DIFFRACTION6EC-4 - 61 - 11
14X-RAY DIFFRACTION6FD-4 - 61 - 11

+
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