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- PDB-3gg7: Crystal structure of an uncharacterized metalloprotein from Deino... -

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Basic information

Entry
Database: PDB / ID: 3gg7
TitleCrystal structure of an uncharacterized metalloprotein from Deinococcus radiodurans
Componentsuncharacterized metalloprotein
Keywordsstructural genomics / unknown function / Plasmid / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
: / 3'-5' ssDNA/RNA exonuclease TatD-like / TatD related DNase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Uncharacterized protein
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Tang, B.K. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized metalloprotein from Deinococcus radiodurans
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Tang, B.K. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized metalloprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9746
Polymers28,4901
Non-polymers4835
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.207, 47.207, 97.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Detailsprobable monomer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein uncharacterized metalloprotein


Mass: 28490.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_C0006 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZH8

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Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.91 Å3/Da / Density % sol: 35.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Hepes pH 7.5, 30% MPD, 500mM ammonium sulfate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 27, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.5→47.207 Å / Num. all: 34252 / Num. obs: 34218 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 17.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.6 / Num. measured all: 51755 / Num. unique all: 5006 / Rsym value: 0.479 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.219 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.807 / SU B: 1.433 / SU ML: 0.053 / SU R Cruickshank DPI: 0.082 / SU Rfree: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; BOUND METAL MODELED AS MN BASED ON XAS STUDIES
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1732 5.1 %RANDOM
Rwork0.183 ---
obs0.184 34157 99.92 %-
all-34184 --
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 max: 52.08 Å2 / Biso mean: 26.12 Å2 / Biso min: 15.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 19 160 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211982
X-RAY DIFFRACTIONr_bond_other_d0.0010.021337
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9612715
X-RAY DIFFRACTIONr_angle_other_deg0.91333235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2795250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04822.20986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0291520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
X-RAY DIFFRACTIONr_mcbond_it0.7521.51223
X-RAY DIFFRACTIONr_mcbond_other0.2021.5492
X-RAY DIFFRACTIONr_mcangle_it1.3521980
X-RAY DIFFRACTIONr_scbond_it2.1583759
X-RAY DIFFRACTIONr_scangle_it3.4884.5731
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 142 -
Rwork0.397 2374 -
all-2516 -
obs-2374 100 %

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