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- PDB-5uuj: Streptomyces sahachiroi DNA glycosylase AlkZ -

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Basic information

Entry
Database: PDB / ID: 5uuj
TitleStreptomyces sahachiroi DNA glycosylase AlkZ
ComponentsAlkZ
KeywordsHYDROLASE / DNA repair / Interstrand crosslink / Azinomycin B / Alkylpurine
Function / homologyDNA glycosylase AlkZ-like / DNA glycosylase AlkZ-like / Azi36
Function and homology information
Biological speciesStreptomyces sahachiroi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.299 Å
AuthorsMullins, E.A. / Eichman, B.F.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517695 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES019625 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR026915 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)T32 ES07028 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of a DNA glycosylase that unhooks interstrand cross-links.
Authors: Mullins, E.A. / Warren, G.M. / Bradley, N.P. / Eichman, B.F.
History
DepositionFeb 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AlkZ


Theoretical massNumber of molelcules
Total (without water)41,6221
Polymers41,6221
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.921, 78.921, 139.401
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein AlkZ / Azi36


Mass: 41622.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sahachiroi (bacteria) / Gene: azi36 / Plasmid: pBG102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Tuner(DE3) / References: UniProt: B4XYC8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% w/v PEG8000, 10 mM Tris-HCl, pH 7.5, 10 magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 25, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.299→50 Å / Num. obs: 21107 / % possible obs: 96.2 % / Redundancy: 12.3 % / Biso Wilson estimate: 21.79 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.035 / Rrim(I) all: 0.123 / Χ2: 1.35 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3812.60.4810.9640.1420.5021.012100
2.38-2.4812.60.3730.9760.110.3881.001100
2.48-2.5912.70.2850.9830.0830.2971.06100
2.59-2.7312.70.2140.990.0630.2231.093100
2.73-2.912.70.1740.9930.0510.1821.144100
2.9-3.1212.70.1390.9950.0410.1451.276100
3.12-3.4412.70.1080.9970.0320.1121.464100
3.44-3.938.60.0930.9960.0310.0982.15465.3
3.93-4.95120.0550.9990.0160.0571.70597.1
4.95-5012.30.0560.9990.0170.0582.08999.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1692phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.299→39.461 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 1037 4.98 %Random
Rwork0.1573 ---
obs0.1594 20828 95.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.79 Å2 / Biso mean: 27.6281 Å2 / Biso min: 8.86 Å2
Refinement stepCycle: final / Resolution: 2.299→39.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 0 245 3127
Biso mean---27.26 -
Num. residues----371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032949
X-RAY DIFFRACTIONf_angle_d0.7694014
X-RAY DIFFRACTIONf_chiral_restr0.028450
X-RAY DIFFRACTIONf_plane_restr0.003518
X-RAY DIFFRACTIONf_dihedral_angle_d13.5991087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2988-2.420.22021480.17042866301497
2.42-2.57160.23221590.17092903306298
2.5716-2.77010.2121520.16692928308099
2.7701-3.04880.25181560.173229663122100
3.0488-3.48970.21541480.171729613109100
3.4897-4.39580.18831230.14132166228973
4.3958-39.46630.14961510.137430013152100
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)
12.7392-2.10680.53243.5598-0.24381.6801-0.076-0.17960.09220.0240.1599-0.0634-0.0572-0.2003-0.10180.1201-0.03530.03630.2026-0.03540.169127.106338.979163.8889
20.44880.63530.67831.24871.41951.62290.0158-0.0348-0.0256-0.0115-0.02530.00380.07030.0260.02280.18510.00590.01760.18730.01660.207833.174625.405553.6011
34.3303-0.47222.63241.14520.87042.94670.25260.4965-0.4207-0.0908-0.0093-0.26020.55660.508-0.26030.34970.06560.01840.2245-0.03430.267937.12588.360343.1813
42.0676-0.35920.74323.78510.84441.73040.16840.628-0.0376-0.6956-0.1153-0.709-0.08280.6519-0.02220.36420.04940.08910.36440.04030.291735.58213.89138.1517
51.7083-1.52280.49662.52890.14571.55970.0472-0.0214-0.1322-0.02940.01810.03140.181-0.051-0.06520.1419-0.0410.00740.15-0.02560.16626.941623.110254.0513
61.72980.69540.98862.64011.42172.25990.0578-0.0694-0.00060.1241-0.2010.46880.2136-0.29930.12880.13850.02330.02090.31-0.01510.253910.770935.556658.5951
73.96240.5393-1.66531.1503-0.07841.7691-0.00390.21990.2171-0.1820.0672-0.0632-0.2049-0.0638-0.06520.18450.00090.02160.18820.0050.186233.936548.439154.0211
84.48710.2636-0.11769.0322-0.94871.39190.0105-0.420.44770.27360.0451-0.1541-0.29350.3134-0.04390.2095-0.08880.02140.3321-0.0920.18845.991949.466163.8862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 40 )A1 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 112 )A41 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 144 )A113 - 144
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 168 )A145 - 168
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 233 )A169 - 233
6X-RAY DIFFRACTION6chain 'A' and (resid 234 through 269 )A234 - 269
7X-RAY DIFFRACTION7chain 'A' and (resid 270 through 346 )A270 - 346
8X-RAY DIFFRACTION8chain 'A' and (resid 347 through 371 )A347 - 371

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