[English] 日本語
Yorodumi
- PDB-4ai5: Crystal structure of Y16F of 3-methyladenine DNA glycosylase I (T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ai5
TitleCrystal structure of Y16F of 3-methyladenine DNA glycosylase I (TAG) in complex with 3-methyladenine
ComponentsDNA-3-METHYLADENINE GLYCOSYLASE I
KeywordsHYDROLASE / 3-METHYLADENINE RECOGNITION / DNA REPAIR / 3-METHYLADENINE TAUTOMER
Function / homologyHypothetical protein; domain 2 / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha / 3-METHYL-3H-PURIN-6-YLAMINE / :
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MSSA476 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsZhu, X. / Naismith, J.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: A Model for 3-Methyladenine Recognition by 3-Methyladenine DNA Glycosylase I (Tag) from Staphylococcus Aureus.
Authors: Zhu, X. / Yan, X. / Carter, L.G. / Liu, H. / Graham, S. / Coote, P.J. / Naismith, J.H.
History
DepositionFeb 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Other
Revision 1.2Jun 20, 2012Group: Other
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
A: DNA-3-METHYLADENINE GLYCOSYLASE I
B: DNA-3-METHYLADENINE GLYCOSYLASE I
C: DNA-3-METHYLADENINE GLYCOSYLASE I
D: DNA-3-METHYLADENINE GLYCOSYLASE I
E: DNA-3-METHYLADENINE GLYCOSYLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,24419
Polymers107,7875
Non-polymers1,45714
Water8,755486
1
A: DNA-3-METHYLADENINE GLYCOSYLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8684
Polymers21,5571
Non-polymers3113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-3-METHYLADENINE GLYCOSYLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8684
Polymers21,5571
Non-polymers3113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA-3-METHYLADENINE GLYCOSYLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8684
Polymers21,5571
Non-polymers3113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA-3-METHYLADENINE GLYCOSYLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7723
Polymers21,5571
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DNA-3-METHYLADENINE GLYCOSYLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8684
Polymers21,5571
Non-polymers3113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.263, 78.813, 179.298
Angle α, β, γ (deg.)90.00, 90.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2007-

HOH

-
Components

#1: Protein
DNA-3-METHYLADENINE GLYCOSYLASE I / 3-METHYLADENINE DNA GLYCOSYLASE I


Mass: 21557.482 Da / Num. of mol.: 5 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MSSA476 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43
References: UniProt: Q6G8R1, DNA-3-methyladenine glycosylase I
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ADK / 3-METHYL-3H-PURIN-6-YLAMINE / 3-METHYLADENINE


Mass: 149.153 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H7N5
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 16 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 16 TO PHE ...ENGINEERED RESIDUE IN CHAIN A, TYR 16 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 16 TO PHE ENGINEERED RESIDUE IN CHAIN C, TYR 16 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 16 TO PHE ENGINEERED RESIDUE IN CHAIN E, TYR 16 TO PHE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.25 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 20, 2011 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 47714 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 11 / % possible all: 89.1

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JG6

2jg6


Resolution: 2.22→179.29 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.03 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21622 2364 5 %RANDOM
Rwork0.18288 ---
obs0.18458 45350 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.736 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.06 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.22→179.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7602 0 80 486 8168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027929
X-RAY DIFFRACTIONr_bond_other_d0.010.025346
X-RAY DIFFRACTIONr_angle_refined_deg1.551.95710736
X-RAY DIFFRACTIONr_angle_other_deg1.6893.00113055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1745939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66824.922384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.225151349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2091515
X-RAY DIFFRACTIONr_chiral_restr0.0890.21111
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218789
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021649
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.218→2.276 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 166 -
Rwork0.193 3043 -
obs--90.04 %
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)
14.1836-0.5195-2.71460.2935-1.323616.00350.1235-0.2932-0.35090.01350.07960.0394-0.08680.0026-0.20310.07640.0021-0.02970.0428-0.0010.137729.6707-32.96112.4488
20.4301-0.12670.18360.54330.17240.6311-0.0195-0.0327-0.01840.03450.04240.02540.0056-0.0511-0.02280.02490.00320.02580.01370.00780.03218.7745-12.72496.1206
30.664-0.617-0.55182.9487-0.12040.6545-0.00190.04230.0331-0.14850.0303-0.03520.0362-0.0524-0.02830.0212-0.0134-0.0140.02220.01070.022326.6104-17.4236-6.8925
410.497910.596615.448210.702315.591322.7606-0.03370.5606-0.21610.05720.4395-0.22670.17380.893-0.40580.29090.18710.03420.3502-0.00960.271331.3905-44.440122.555
51.03560.10640.21650.92460.22460.61360.020.00340.06060.0302-0.00250.007-0.0440.0044-0.01750.05050.02680.01730.02560.00190.013510.7449-32.822123.7391
62.2726-1.09690.12571.40160.40611.7609-0.0323-0.11770.12330.13550.0945-0.1477-0.03650.2228-0.06220.0719-0.0019-0.02130.0384-0.01810.032523.0984-32.531533.2181
71.3357-0.70841.35322.1186-0.57231.43630.1042-0.15-0.15590.1853-0.02540.07780.1069-0.1157-0.07880.0903-0.00510.00860.11340.07270.161811.9346-10.647285.2251
81.1859-0.50430.13031.4794-0.03250.4393-0.0107-0.0495-0.04090.01320.01280.0282-0.0664-0.0656-0.00210.04070.0347-0.00660.0358-0.01480.02849.49673.161478.1309
92.2684-0.98290.58332.8236-0.3771.7782-0.002-0.0109-0.303-0.19640.03170.26060.1303-0.1206-0.02960.04170.01440.00190.0602-0.01350.10217.0047-7.874475.4675
100.7914-0.0215-0.87351.17060.25441.6335-0.1083-0.3502-0.08340.17050.0996-0.15120.21640.3690.00880.0780.0831-0.02360.19810.02720.0371-7.6476-11.795148.2027
111.16510.33710.43051.68240.51532.6703-0.232-0.2707-0.02740.19740.16920.08080.09380.18940.06280.10620.10020.02190.17170.03530.0089-17.4199-10.918154.4913
121.5454-0.3261-0.78170.38080.18713.0481-0.0836-0.0683-0.22120.08740.01280.11140.1926-0.16340.07090.08590.02780.01910.04330.0150.0531-18.406-15.16737.6727
131.9672-0.0459-0.79592.3959-1.8583.05480.14740.2419-0.3296-0.0858-0.2183-0.03830.10960.07150.07090.06330.0621-0.01630.0925-0.03750.087430.1902-18.916166.2748
141.4745-0.5570.271.3839-0.12351.45120.22720.48520.0367-0.3725-0.36040.0198-0.04540.09020.13310.150.1475-0.00380.2259-0.00710.03624.6197-9.149455.6285
151.4117-1.49710.03725.7337-2.3394.07980.08630.11040.12920.2032-0.205-0.6617-0.14740.72070.11870.05470.0139-0.00530.1738-0.01090.120636.9826-13.124972.0287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 12
2X-RAY DIFFRACTION2A13 - 125
3X-RAY DIFFRACTION3A126 - 186
4X-RAY DIFFRACTION4B1 - 9
5X-RAY DIFFRACTION5B10 - 126
6X-RAY DIFFRACTION6B127 - 186
7X-RAY DIFFRACTION7C1 - 31
8X-RAY DIFFRACTION8C32 - 149
9X-RAY DIFFRACTION9C150 - 186
10X-RAY DIFFRACTION10D-1 - 77
11X-RAY DIFFRACTION11D78 - 122
12X-RAY DIFFRACTION12D123 - 186
13X-RAY DIFFRACTION13E-1 - 32
14X-RAY DIFFRACTION14E33 - 167
15X-RAY DIFFRACTION15E168 - 186

+
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