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- PDB-2h56: Crystal structure of DNA-3-methyladenine glycosidase (10174367) f... -

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Basic information

Entry
Database: PDB / ID: 2h56
TitleCrystal structure of DNA-3-methyladenine glycosidase (10174367) from Bacillus halodurans at 2.55 A resolution
ComponentsDNA-3-methyladenine glycosidase
KeywordsHYDROLASE / 10174367 / DNA-3-methyladenine glycosidase / EC 3.2.2.- / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / base-excision repair
Similarity search - Function
Endonuclease Iii, domain 2 - #40 / Endonuclease Iii, domain 2 / HhH-GPD superfamily base excision DNA repair protein / Hypothetical protein; domain 2 / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-3-methyladenine glycosidase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of DNA-3-methyladenine glycosidase (10174367) from Bacillus halodurans at 2.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: 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: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-3-methyladenine glycosidase
B: DNA-3-methyladenine glycosidase
C: DNA-3-methyladenine glycosidase


Theoretical massNumber of molelcules
Total (without water)79,2463
Polymers79,2463
Non-polymers00
Water72140
1
A: DNA-3-methyladenine glycosidase


Theoretical massNumber of molelcules
Total (without water)26,4151
Polymers26,4151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-3-methyladenine glycosidase


Theoretical massNumber of molelcules
Total (without water)26,4151
Polymers26,4151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA-3-methyladenine glycosidase


Theoretical massNumber of molelcules
Total (without water)26,4151
Polymers26,4151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.752, 141.752, 85.949
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
12A
22B

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111MSETHRAA1 - 3513 - 47
211MSETHRBB1 - 3513 - 47
311MSETHRCC1 - 3513 - 47
421THRHISAA138 - 217150 - 229
521THRHISBB138 - 217150 - 229
621THRGLNCC138 - 220150 - 232
112LYSGLNAA36 - 13648 - 148
212LYSGLNBB36 - 13648 - 148

NCS ensembles :
ID
1
2

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Components

#1: Protein DNA-3-methyladenine glycosidase


Mass: 26415.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10174367 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KC25, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.1
Details: 0.2M NaF, 20.0% PEG-3350, No Buffer, pH 7.1, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0163, 0.9798
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.01631
20.97981
ReflectionResolution: 2.54→46.42 Å / Num. obs: 31756 / % possible obs: 93.4 % / Redundancy: 6.49 % / Biso Wilson estimate: 54.685 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.54-2.6320.3925582279386.1
2.63-2.7420.3072.66275311193.3
2.74-2.862.90.3673.68681298394.8
2.86-3.018.10.4745.5260923203100
3.01-3.28.20.3227.5269063271100
3.2-3.448.20.18112.4260283176100
3.44-3.798.10.10618.6268073290100
3.79-4.338.20.06528264493242100
4.33-5.448.10.05830.8264593284100
5.44-46.47.90.03840.426908340399.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHELXphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.55→46.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 19.51 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.257
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE ARE THREE MONOMERS IN THE ASSYMMETRIC UNIT. CHAIN A AND B ARE VERY SIMILAR TO EACH OTHER. CHAIN C DIFFERS FROM A/B DUE TO INTER- ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE ARE THREE MONOMERS IN THE ASSYMMETRIC UNIT. CHAIN A AND B ARE VERY SIMILAR TO EACH OTHER. CHAIN C DIFFERS FROM A/B DUE TO INTER-DOMAIN MOVEMENT. THE MOVEMENT IN THE MONOMER C CAN BE DESCRIBED BY ROTATION OF ~23 DEGREE AROUND RESIDUES 33-34,110-126. 3. THERE ARE SIGNIFICANT DISORDER IN THE DOMAIN C38-148. THE FOLLOWING RESIDUES ARE NOT MODELED DESPITE PRESENCE DISORDERED DENSITY: C81, C115-121, C130-133. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1606 5.1 %RANDOM
Rwork0.196 ---
obs0.198 31729 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.814 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20.81 Å20 Å2
2--1.61 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4815 0 0 40 4855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224911
X-RAY DIFFRACTIONr_bond_other_d0.0010.023259
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9536648
X-RAY DIFFRACTIONr_angle_other_deg0.9337924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16523.385195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78815787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6761527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_nbd_refined0.2360.21148
X-RAY DIFFRACTIONr_nbd_other0.1810.23160
X-RAY DIFFRACTIONr_nbtor_refined0.1940.22436
X-RAY DIFFRACTIONr_nbtor_other0.0880.22509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.211
X-RAY DIFFRACTIONr_mcbond_it1.69333223
X-RAY DIFFRACTIONr_mcbond_other0.36731310
X-RAY DIFFRACTIONr_mcangle_it2.88554977
X-RAY DIFFRACTIONr_scbond_it5.48481963
X-RAY DIFFRACTIONr_scangle_it7.528111671
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1453LOOSE POSITIONAL0.645
12B1453LOOSE POSITIONAL0.615
13C1453LOOSE POSITIONAL0.555
11A1453LOOSE THERMAL3.4610
12B1453LOOSE THERMAL2.6810
13C1453LOOSE THERMAL3.5410
21A1213LOOSE POSITIONAL0.445
21A1213LOOSE THERMAL2.7810
LS refinement shellResolution: 2.545→2.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 119 -
Rwork0.306 2045 -
obs-2164 91.23 %
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)
14.1316-2.00250.83486.10360.20973.79130.0781-0.4822-0.22070.2274-0.15730.4530.1806-0.64360.0792-0.43890.0264-0.075-0.1065-0.0266-0.273921.820634.650517.8407
24.9140.67370.52372.04020.28563.6895-0.14260.07440.2318-0.08540.0889-0.02270.20490.18750.0538-0.3310.1233-0.0917-0.3599-0.0748-0.27129.441941.1646-6.144
32.4046-0.122-1.063910.4685.57016.14840.1351-0.0615-0.00390.77350.394-1.26110.6770.2956-0.5291-0.2694-0.0351-0.1202-0.2879-0.1508-0.1026-6.94855.09217.438
42.12280.90082.26143.35812.83895.86680.13870.1494-0.07090.1211-0.17430.03270.4214-0.15050.0356-0.2119-0.0307-0.0004-0.33150.0036-0.3138-7.516577.651235.3978
53.59760.02870.11654.40771.49155.21970.18650.1567-0.0045-0.5441-0.04310.3351-0.292-0.2062-0.1434-0.20710.08780.0101-0.29320.0286-0.24489.971761.502961.0275
63.9203-1.4376-3.28423.43520.802311.04060.17610.05280.43380.11390.2567-0.7855-0.7911.2574-0.43290.19790.0283-0.04790.171-0.177-0.03223.416757.987538.8825
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 3712 - 49
21AA149 - 217161 - 229
32AA38 - 14850 - 160
43BB1 - 3713 - 49
53BB149 - 217161 - 229
64BB38 - 14850 - 160
75CC1 - 3713 - 49
85CC149 - 220161 - 232
96CC38 - 14850 - 160

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