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- PDB-3qd7: Crystal structure of YdaL, a stand-alone small MutS-related prote... -

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Basic information

Entry
Database: PDB / ID: 3qd7
TitleCrystal structure of YdaL, a stand-alone small MutS-related protein from Escherichia coli
ComponentsUncharacterized protein ydaL
KeywordsHYDROLASE / alpha/beta/alpha fold / endonuclease
Function / homology
Function and homology information


DNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding
Similarity search - Function
: / Ribosomal Protein S8; Chain: A, domain 1 - #110 / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable DNA endonuclease SmrA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGui, W.J. / Qu, Q.H. / Chen, Y.Y. / Wang, M. / Zhang, X.E. / Bi, L.J. / Jiang, T.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structure of YdaL, a stand-alone small MutS-related protein from Escherichia coli.
Authors: Gui, W.J. / Qu, Q.H. / Chen, Y.Y. / Wang, M. / Zhang, X.E. / Bi, L.J. / Jiang, T.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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

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Assembly

Deposited unit
X: Uncharacterized protein ydaL


Theoretical massNumber of molelcules
Total (without water)15,4431
Polymers15,4431
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.517, 34.833, 40.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein ydaL


Mass: 15442.687 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ydaL, b1340, JW1334 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76053
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1943.89
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, hanging drop61.5M ammonium sulfate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
2892vapor diffusion, hanging drop61.5M ammonium sulfate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.979
SYNCHROTRONSSRF BL17U21.5028
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDJan 31, 2010
MARMOSAIC 225 mm CCD2CCDMay 16, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni MIRRORSINGLE WAVELENGTHMx-ray1
2Ni MIRRORSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.50281
ReflectionResolution: 2.3→50 Å / Num. all: 6306 / Num. obs: 6306 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.061 / Rsym value: 0.064 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 8.26 / Num. unique all: 587 / Rsym value: 0.242 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 2.3→47.76 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.105 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24358 323 5.2 %RANDOM
Rwork0.22415 ---
all0.22516 6306 --
obs0.22516 6306 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.485 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 0 21 1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9591437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8775130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29723.20853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48715185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4241510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021812
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 26 -
Rwork0.21 382 -
obs--88.31 %

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