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- PDB-5h9i: Crystal structure of Geobacter metallireducens SMUG1 with xanthine -

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Basic information

Entry
Database: PDB / ID: 5h9i
TitleCrystal structure of Geobacter metallireducens SMUG1 with xanthine
ComponentsGeobacter metallireducens SMUG1
KeywordsHYDROLASE / SMUG1 / DNA damage / base excision repair / substrate specificity
Function / homology
Function and homology information


single-strand selective uracil DNA N-glycosylase activity / base-excision repair / DNA binding
Similarity search - Function
Single-strand selective monofunctional uracil DNA glycosylase / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / ISOPROPYL ALCOHOL / PENTANOIC ACID / XANTHINE / Uracil-DNA glycosylase-like domain-containing protein
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsXie, W. / Cao, W. / Zhang, Z. / Shen, J.
Funding support China, 4items
OrganizationGrant numberCountry
Science and Technology Program of Guangzhou201504010025 China
Foundation of Key Laboratory of Gene Engineering of the Ministry of Education201502 China
Guangdong Innovative Research Team2011Y038 China
the Fundamental Research Funds for the Central Universities15lgjc02 China
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structural Basis of Substrate Specificity in Geobacter metallireducens SMUG1
Authors: Zhang, Z. / Shen, J. / Yang, Y. / Li, J. / Cao, W. / Xie, W.
History
DepositionDec 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geobacter metallireducens SMUG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7968
Polymers26,1271
Non-polymers6697
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.972, 64.339, 45.654
Angle α, β, γ (deg.)90.00, 111.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

21A-509-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Geobacter metallireducens SMUG1


Mass: 26126.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: Gmet_0095 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q39ZI0

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Non-polymers , 6 types, 184 molecules

#2: Chemical ChemComp-XAN / XANTHINE / Xanthine


Mass: 152.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-LEA / PENTANOIC ACID / VALERIC ACID / Valeric acid


Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 16-21% PEG6000, 0.2M NaCl or (NH4)2SO4 and 0.1M MES (pH 6.0)

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 40018 / % possible obs: 98.9 % / Observed criterion σ(I): 2.6 / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.6 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OE4

1oe4


Resolution: 1.501→38.051 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 1983 5.01 %
Rwork0.1715 --
obs0.1732 39571 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→38.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 44 177 2051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0271934
X-RAY DIFFRACTIONf_angle_d2.3082627
X-RAY DIFFRACTIONf_dihedral_angle_d12.842691
X-RAY DIFFRACTIONf_chiral_restr0.144278
X-RAY DIFFRACTIONf_plane_restr0.015346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5012-1.53880.27111150.25652617X-RAY DIFFRACTION96
1.5388-1.58040.261530.23262643X-RAY DIFFRACTION98
1.5804-1.62690.26351440.21852647X-RAY DIFFRACTION98
1.6269-1.67940.21851260.19742692X-RAY DIFFRACTION98
1.6794-1.73940.22931450.19542663X-RAY DIFFRACTION98
1.7394-1.8090.20991410.18122677X-RAY DIFFRACTION99
1.809-1.89140.19661320.18052690X-RAY DIFFRACTION99
1.8914-1.99110.19741490.17172681X-RAY DIFFRACTION99
1.9911-2.11580.17941520.17412687X-RAY DIFFRACTION99
2.1158-2.27920.19121360.1642720X-RAY DIFFRACTION100
2.2792-2.50850.21871540.16872676X-RAY DIFFRACTION100
2.5085-2.87140.1941400.1732729X-RAY DIFFRACTION100
2.8714-3.61720.18061450.15692739X-RAY DIFFRACTION100
3.6172-38.06370.21741510.1582727X-RAY DIFFRACTION98

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