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- PDB-5h93: Crystal structure of Geobacter metallireducens SMUG1 -

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Basic information

Entry
Database: PDB / ID: 5h93
TitleCrystal structure of Geobacter metallireducens SMUG1
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 / oxidized pyrimidine nucleobase lesion 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
Uracil-DNA glycosylase-like domain-containing protein
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.176 Å
AuthorsXie, W. / Cao, W. / Zhang, Z. / Shen, J.
Funding support China, 4items
OrganizationGrant numberCountry
Guangdong Innovative Research Team Program2011Y038 China
Foundation of Key Laboratory of Gene Engineering of the Ministry of Education201502 China
Science and Technology Program of Guangzhou201504010025 China
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 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geobacter metallireducens SMUG1
B: Geobacter metallireducens SMUG1
C: Geobacter metallireducens SMUG1
D: Geobacter metallireducens SMUG1


Theoretical massNumber of molelcules
Total (without water)104,5084
Polymers104,5084
Non-polymers00
Water7,422412
1
A: Geobacter metallireducens SMUG1


Theoretical massNumber of molelcules
Total (without water)26,1271
Polymers26,1271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Geobacter metallireducens SMUG1


Theoretical massNumber of molelcules
Total (without water)26,1271
Polymers26,1271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Geobacter metallireducens SMUG1


Theoretical massNumber of molelcules
Total (without water)26,1271
Polymers26,1271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Geobacter metallireducens SMUG1


Theoretical massNumber of molelcules
Total (without water)26,1271
Polymers26,1271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.354, 57.950, 90.596
Angle α, β, γ (deg.)70.80, 71.87, 75.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Geobacter metallireducens SMUG1


Mass: 26126.951 Da / Num. of mol.: 4
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q39ZI0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 54021 / % possible obs: 94.6 % / Observed criterion σ(I): 1.46 / Redundancy: 2.9 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.7
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 1.46 / % possible all: 88.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OE4

1oe4


Resolution: 2.176→32.5 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2589 5.07 %
Rwork0.221 --
obs0.2227 51035 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.176→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6962 0 0 412 7374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037152
X-RAY DIFFRACTIONf_angle_d0.7499756
X-RAY DIFFRACTIONf_dihedral_angle_d11.7152483
X-RAY DIFFRACTIONf_chiral_restr0.0271072
X-RAY DIFFRACTIONf_plane_restr0.0031294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1764-2.21830.31891360.27472315X-RAY DIFFRACTION80
2.2183-2.26360.27311360.26422681X-RAY DIFFRACTION95
2.2636-2.31280.30961480.25922752X-RAY DIFFRACTION96
2.3128-2.36660.31991370.25322741X-RAY DIFFRACTION96
2.3666-2.42570.28751300.24642778X-RAY DIFFRACTION96
2.4257-2.49130.26291380.24832753X-RAY DIFFRACTION96
2.4913-2.56460.271340.24272734X-RAY DIFFRACTION97
2.5646-2.64730.29971640.23552780X-RAY DIFFRACTION97
2.6473-2.74190.281230.23452767X-RAY DIFFRACTION97
2.7419-2.85160.2651660.23852729X-RAY DIFFRACTION97
2.8516-2.98130.27951370.24692723X-RAY DIFFRACTION96
2.9813-3.13840.3011450.24832715X-RAY DIFFRACTION94
3.1384-3.33480.28661430.24312714X-RAY DIFFRACTION95
3.3348-3.5920.26211610.23182684X-RAY DIFFRACTION95
3.592-3.95290.2191390.19392695X-RAY DIFFRACTION94
3.9529-4.52360.23711480.18982663X-RAY DIFFRACTION93
4.5236-5.69420.20451670.19722641X-RAY DIFFRACTION94
5.6942-32.50390.20511370.18942581X-RAY DIFFRACTION91

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