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Basic information

Entry
Database: PDB / ID: 4aia
TitleThe structural basis of 3-methyladenine recognition by 3- methyladenine DNA glycosylase I (TAG) from Staphylococcus aureus
ComponentsDNA-3-METHYLADENINE GLYCOSYLASE I
KeywordsHYDROLASE / 3-METHYLADENINE RECOGNITION / DNA REPAIR
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYan, 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 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Other
Revision 1.2Jun 20, 2012Group: Other
Revision 1.3Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)109,32419
Polymers107,8675
Non-polymers1,45714
Water16,700927
1
A: DNA-3-METHYLADENINE GLYCOSYLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8844
Polymers21,5731
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)21,7883
Polymers21,5731
Non-polymers2152
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)21,8844
Polymers21,5731
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)21,7883
Polymers21,5731
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)21,9805
Polymers21,5731
Non-polymers4074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.000, 78.590, 179.810
Angle α, β, γ (deg.)90.00, 90.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21A-2109-

HOH

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Components

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


Mass: 21573.484 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MSSA476 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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.: 927 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: QUANTUM 4 / Detector: CCD / Date: Sep 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→29.6 Å / Num. obs: 92544 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.8 / % possible all: 91.6

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Processing

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

2jg6


Resolution: 1.8→28.19 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.544 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.HYDROGENS HAVE BEEN USED IF PRESENT IN INPUT. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 4654 5 %RANDOM
Rwork0.17846 ---
obs0.18045 87884 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.01 Å2
2---0.07 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7598 0 80 927 8605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.96110807
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0085956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36924.922384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.185151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9581515
X-RAY DIFFRACTIONr_chiral_restr0.0830.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216109
X-RAY DIFFRACTIONr_gen_planes_other
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 308 -
Rwork0.233 5568 -
obs--85.51 %
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)
10.6536-0.22110.00090.91660.14240.4743-0.0191-0.0712-0.0050.07540.02750.0627-0.0065-0.0471-0.00850.01560.00250.0130.01430.00860.059820.1189-14.72325.7929
20.7034-0.5121-0.10231.95890.14710.55110.02110.0799-0.0167-0.16220.01780.0131-0.00130.0035-0.03890.0246-0.0049-0.00360.01450.0050.04426.8658-17.4431-6.8932
31.23620.08690.25261.1580.22130.8596-0.01970.02860.0223-0.02190.02350.00980.01580.0176-0.00380.06390.01770.00430.0094-0.00460.037711.0168-35.732922.3995
41.8065-0.3569-0.05441.05040.28951.3048-0.0297-0.1810.17880.1490.0757-0.20140.02150.172-0.0460.09050.0214-0.01830.0567-0.03330.085722.0116-29.760933.1949
52.2684-0.97760.14542.51040.23321.0596-0.0502-0.210.04370.12940.0499-0.094-0.0954-0.01130.00030.12590.04180.01390.1383-0.01770.088112.80623.46583.0936
62.3675-1.26140.24493.16570.50611.21490.06990.0878-0.4922-0.1406-0.06840.4630.0507-0.1589-0.00140.11170.0285-0.01610.1599-0.0340.19614.9274-7.816473.7138
70.8374-0.0405-0.40531.03750.02152.5061-0.05-0.4062-0.05180.2050.0382-0.04250.11510.13840.01180.15210.0742-0.01980.25550.03790.1134-11.5511-11.554350.5746
82.4851-0.5987-0.74210.61580.33152.8462-0.0417-0.1886-0.18560.05190.03180.0590.1961-0.17680.00990.12930.02770.00670.09350.0280.1089-18.3709-14.563637.9008
92.4746-0.83291.14921.9292-0.06221.9730.31420.8215-0.1282-0.5038-0.37560.10010.030.33240.06130.26010.1908-0.00670.4309-0.07810.119925.7508-13.599755.4871
102.8644-1.18491.07842.6489-0.49343.15540.05270.43360.2871-0.1396-0.2285-0.1623-0.25350.27820.17570.12910.0440.01110.19790.02930.139829.9891-6.121667.3073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 125
2X-RAY DIFFRACTION2A126 - 186
3X-RAY DIFFRACTION3B1 - 107
4X-RAY DIFFRACTION4B108 - 185
5X-RAY DIFFRACTION5C1 - 107
6X-RAY DIFFRACTION6C108 - 186
7X-RAY DIFFRACTION7D-1 - 125
8X-RAY DIFFRACTION8D126 - 186
9X-RAY DIFFRACTION9E-1 - 125
10X-RAY DIFFRACTION10E126 - 186

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