[English] 日本語
Yorodumi
- PDB-5cle: Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cle
TitleAlkylpurine DNA glycosylase AlkD bound to DNA containing an abasic-site analog and a free 3-methyladenine nucleobase
Components
  • AlkD
  • DNA (5'-D(*CP*CP*CP*GP*AP*(3DR)P*AP*GP*TP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')
KeywordsHYDROLASE/DNA / DNA glycosylase / HEAT-like repeat / protein-DNA complex / HYDROLASE-DNA complex
Function / homology
Function and homology information


Leucine-rich Repeat Variant - #90 / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
3-METHYL-3H-PURIN-6-YLAMINE / DNA / DNA (> 10) / DNA alkylation repair protein / DNA alkylation repair enzyme
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMullins, E.A. / Eichman, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1122098 United States
CitationJournal: Nature / Year: 2015
Title: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Authors: Mullins, E.A. / Shi, R. / Parsons, Z.D. / Yuen, P.K. / David, S.S. / Igarashi, Y. / Eichman, B.F.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AlkD
B: DNA (5'-D(*CP*CP*CP*GP*AP*(3DR)P*AP*GP*TP*CP*CP*G)-3')
C: DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9214
Polymers35,7723
Non-polymers1491
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-12 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.492, 93.288, 48.162
Angle α, β, γ (deg.)90.000, 112.840, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein AlkD


Mass: 28578.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: IKE_03968 / Plasmid: pBG103 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174
References: UniProt: R8GWR7, UniProt: Q816E8*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: DNA chain DNA (5'-D(*CP*CP*CP*GP*AP*(3DR)P*AP*GP*TP*CP*CP*G)-3')


Mass: 3499.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')


Mass: 3694.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ADK / 3-METHYL-3H-PURIN-6-YLAMINE / 3-METHYLADENINE


Mass: 149.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 17% w/v PEG4000, 42 mM sodium acetate, pH 4.6, 85 mM ammonium acetate, 5% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 2, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 32574 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 18.89 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.074 / Χ2: 1.172 / Net I/av σ(I): 23.195 / Net I/σ(I): 11.7 / Num. measured all: 161136
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.794.60.4433.38332400.8920.2280.51.00899.6
1.79-1.864.80.35132400.9310.1770.3941.07499.9
1.86-1.954.90.26332440.9560.1310.2941.10299.9
1.95-2.054.90.17832370.980.0890.1991.16899.9
2.05-2.184.90.11932550.9910.0590.1331.226100
2.18-2.3550.08832550.9940.0440.0991.29100
2.35-2.5850.06832650.9960.0330.0761.227100
2.58-2.965.10.05932650.9960.0290.0651.022100
2.96-3.735.10.06332720.9960.0310.071.382100
3.73-5050.03433010.9980.0170.0381.19199.5

-
Processing

Software
NameClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BVS

3bvs


Resolution: 1.73→40.079 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 1626 5 %Random selection
Rwork0.1547 30913 --
obs0.1566 32539 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.04 Å2 / Biso mean: 26.0956 Å2 / Biso min: 9.87 Å2
Refinement stepCycle: final / Resolution: 1.73→40.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 476 11 328 2766
Biso mean--24.83 35.46 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072562
X-RAY DIFFRACTIONf_angle_d1.0093574
X-RAY DIFFRACTIONf_chiral_restr0.044385
X-RAY DIFFRACTIONf_plane_restr0.006370
X-RAY DIFFRACTIONf_dihedral_angle_d17.902984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.7304-1.78130.2881345.11450.2106248696
1.7813-1.83880.25851375.04050.20062581100
1.8388-1.90450.22231334.92590.18312567100
1.9045-1.98080.23671405.1490.17652579100
1.9808-2.07090.23131324.88890.1712568100
2.0709-2.18010.19591314.85540.15392567100
2.1801-2.31670.21631354.95960.15372587100
2.3167-2.49550.19671385.09410.15572571100
2.4955-2.74660.21261374.99270.16942607100
2.7466-3.14390.20881344.93190.16112583100
3.1439-3.96040.15691364.98350.14362593100
3.9604-40.08980.14771395.03080.1266262499
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)
12.151-1.89261.31538.8667-7.26746.3370.07150.08260.26570.3007-0.04450.0418-0.60270.0721-0.0280.2514-0.01770.03490.1574-0.01680.197525.616922.393321.3777
25.5003-1.1159-3.51363.92191.92136.5879-0.1506-0.3555-0.08070.17110.1612-0.14080.0450.39090.00770.1062-0.0005-0.02070.12330.00630.096738.15058.471226.3169
37.2452-4.54114.41857.5999-5.34987.33650.0577-0.2276-0.2688-0.05630.25460.62950.0862-0.4828-0.21050.1338-0.0283-0.00290.1817-0.01060.13620.449212.277919.84
46.258-1.04232.11663.3689-2.41026.22-0.07210.29730.26660.07640.01080.1782-0.37970.04620.08930.19520.0110.02350.0803-0.00590.147828.351121.707711.0292
58.0102-0.04284.88222.18910.00043.2890.06950.4008-0.2272-0.06680.06210.12350.06770.0604-0.13650.1304-0.00180.01190.1713-0.00520.117127.574613.233610.4112
63.6651-4.28424.58727.0316-5.07766.978-0.106-0.15410.0736-0.2678-0.0147-0.1505-0.152-0.22440.11250.162-0.0040.02960.1225-0.02090.107234.637116.4345-0.0645
71.1203-0.21640.20951.117-0.09186.59690.03950.0250.0099-0.02510.03560.04280.1294-0.0911-0.07270.134-0.00110.01250.0728-0.00460.13339.48039.36880.3308
84.28332.35882.94556.56333.57896.71130.0773-0.0406-0.1858-0.1546-0.00160.17440.2585-0.1953-0.06630.1323-0.00390.01370.08810.02190.0939.41371.4366-1.0052
97.95170.88510.72395.54630.58175.67640.08620.3153-0.2567-0.28030.0912-0.13940.22130.1881-0.13970.15370.01970.01590.0547-0.00350.102149.7545-0.7302-3.8031
101.106-0.2686-0.25555.80031.23490.9252-0.09150.0072-0.17760.13730.03880.04080.20650.02620.03710.1958-0.00640.01590.1053-0.00110.110145.7209-11.82171.7491
110.1056-0.5186-0.22863.11490.54423.1346-0.4698-0.5077-0.66570.08120.2749-0.17440.0718-0.1328-0.09990.18030.07980.0690.27570.08590.299340.6423-8.588119.2477
125.9961-4.121-2.41223.71732.26821.415-0.44780.4183-0.78790.27420.03470.14380.45250.74190.02650.14090.08530.08610.64610.27030.592547.82-12.656619.7879
133.37572.91422.24222.95471.2023.2097-0.33750.0307-0.6451-0.24970.36480.8565-0.7848-0.95090.15510.29130.0897-0.0280.4393-0.04380.379829.3551-4.079916.7056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 38 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 53 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 73 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 90 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 103 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 104 through 143 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 144 through 162 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 163 through 178 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 179 through 229 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 12 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 6 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 7 through 12 )C0

+
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