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- PDB-6onw: Crystal structure of Sel1 repeat protein from Oxalobacter formigenes -

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Basic information

Entry
Database: PDB / ID: 6onw
TitleCrystal structure of Sel1 repeat protein from Oxalobacter formigenes
ComponentsSel1 repeat protein
KeywordsHYDROLASE / Sel1 repeat / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology: / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / beta-lactamase activity / beta-lactamase / Tetratricopeptide-like helical domain superfamily / DI(HYDROXYETHYL)ETHER / Sel1 repeat protein
Function and homology information
Biological speciesOxalobacter formigenes OXCC13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.951 Å
AuthorsChang, C. / Tesar, C. / Endres, M. / Babnigg, G. / Hassan, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of Sel1 repeat protein from Oxalobacter formigenes
Authors: Chang, C. / Tesar, C. / Endres, M. / Babnigg, G. / Hassan, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Sel1 repeat protein
B: Sel1 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8266
Polymers85,4452
Non-polymers3804
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint4 kcal/mol
Surface area31050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.773, 74.079, 194.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sel1 repeat protein


Mass: 42722.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00639 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X8T5, beta-lactamase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-Cl, 30% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 21711 / % possible obs: 98.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 57.89 Å2 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.081 / Rrim(I) all: 0.189 / Χ2: 0.87 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-33.90.739920.5970.3930.8330.84592.8
3-3.064.40.72310020.6340.3680.8160.84694.5
3.06-3.114.80.65210450.6610.3170.7290.86397.9
3.11-3.185.10.65210960.7050.310.7270.89198.4
3.18-3.255.20.58410430.6630.2820.6520.87998.8
3.25-3.325.40.47110830.810.2220.5230.89799.3
3.32-3.415.30.39510680.8450.1890.4410.85499.6
3.41-3.55.40.34810860.8830.1670.3880.87699.5
3.5-3.65.30.29910690.8810.1450.3340.85699.6
3.6-3.724.90.23810910.9170.1190.2680.82399.5
3.72-3.855.60.20710930.9450.0970.2290.827100
3.85-45.60.1810710.9530.0850.20.87399.9
4-4.195.70.15110960.9720.070.1670.85699.5
4.19-4.415.50.12511120.9780.0580.1380.82499.6
4.41-4.685.40.11410890.9790.0540.1260.86499.9
4.68-5.0450.1110910.9740.0540.1230.85599
5.04-5.555.60.12411100.9760.0580.1380.86799.9
5.55-6.355.50.10711320.9760.050.1190.86799.3
6.35-850.08111270.9770.0390.0910.86298.9
8-504.90.06312150.9910.0310.0711.05998.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.951→39.99 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.04
RfactorNum. reflection% reflection
Rfree0.2593 1012 4.77 %
Rwork0.211 --
obs0.2133 20798 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 180.04 Å2 / Biso mean: 53.9457 Å2 / Biso min: 16.06 Å2
Refinement stepCycle: final / Resolution: 2.951→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5336 0 25 11 5372
Biso mean--58.29 39.01 -
Num. residues----689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025491
X-RAY DIFFRACTIONf_angle_d0.4257414
X-RAY DIFFRACTIONf_chiral_restr0.035761
X-RAY DIFFRACTIONf_plane_restr0.004960
X-RAY DIFFRACTIONf_dihedral_angle_d10.2343234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9512-3.0310.31831050.31242186229172
3.031-3.12020.42491270.30992379250681
3.1202-3.22080.42051570.31072584274186
3.2208-3.33590.3611720.29062646281890
3.3359-3.46940.26051420.25392844298694
3.4694-3.62720.34441180.22942925304397
3.6272-3.81830.28741290.22052896302597
3.8183-4.05730.18961530.199230373190100
4.0573-4.37020.21261490.17452979312899
4.3702-4.80930.22351330.16112957309099
4.8093-5.50370.22211360.18652970310699
5.5037-6.92820.231560.19672950310698
6.9282-39.99330.21981400.1862917305797

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