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

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Basic information

Entry
Database: PDB / ID: 6ork
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
Function and homology information


beta-lactamase activity / beta-lactamase
Similarity search - Function
: / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesOxalobacter formigenes OXCC13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 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 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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
C: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)85,2013
Polymers85,2013
Non-polymers00
Water00
1
A: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)28,4001
Polymers28,4001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)28,4001
Polymers28,4001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)28,4001
Polymers28,4001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.926, 103.368, 122.709
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: 28400.473 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00863 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X9F9, beta-lactamase
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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10 mM tri-sodium citrate, 33% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16196 / % possible obs: 98.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 48.91 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Χ2: 0.861 / Net I/σ(I): 6.7 / Num. measured all: 93909
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.053.80.8936630.5980.4611.0120.96283.2
3.05-3.114.10.8397330.6850.4230.9460.93989.3
3.11-3.174.40.7147630.7640.3490.7990.90694.7
3.17-3.234.80.6227890.8470.2930.6910.94397.3
3.23-3.35.20.5347990.9050.2460.590.90799.1
3.3-3.385.50.4398130.9240.1980.4830.9499.8
3.38-3.465.70.3838100.9590.1710.420.9399.8
3.46-3.565.50.3018020.9660.1370.3320.91199.4
3.56-3.665.90.2358220.9750.1040.2570.861100
3.66-3.786.60.1947930.9880.0810.210.88799.6
3.78-3.916.60.1558330.9850.0650.1690.911100
3.91-4.076.70.1158070.9920.0480.1250.845100
4.07-4.266.50.0888180.9950.0370.0960.859100
4.26-4.486.40.0718340.9960.030.0770.79799.8
4.48-4.765.80.0658260.9940.0280.0710.78699.5
4.76-5.136.80.0688300.9950.0280.0740.787100
5.13-5.646.70.0658350.9940.0270.0710.78399.8
5.64-6.466.40.0588410.9950.0250.0630.809100
6.46-8.135.90.0438630.9940.0190.0470.8399.9
8.13-505.70.0349220.9980.0160.0370.81899.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 3→43.585 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.42
RfactorNum. reflection% reflection
Rfree0.2538 701 4.99 %
Rwork0.2091 --
obs0.2114 14231 81.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.73 Å2 / Biso mean: 43.6273 Å2 / Biso min: 10.42 Å2
Refinement stepCycle: final / Resolution: 3→43.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5751 0 0 0 5751
Num. residues----737
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9916-3.11140.4137640.33271170123436
3.1114-3.2530.3022820.29351645172751
3.253-3.42440.3758890.26012249233868
3.4244-3.63880.27831440.23742742288685
3.6388-3.91960.30651600.2233171333198
3.9196-4.31380.25441730.188732173390100
4.3138-4.93720.25471970.177531943391100
4.9372-6.21750.23091870.198832343421100
6.2175-43.58940.17951570.18633231338899

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