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- PDB-6ok3: Crystal structure of Sel1 repeat protein from Oxalobacter formigenes -

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Basic information

Entry
Database: PDB / ID: 6ok3
TitleCrystal structure of Sel1 repeat protein from Oxalobacter formigenes
Components(Sel1 repeat protein) x 2
KeywordsHYDROLASE / Sel1 repeat / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologySel1 repeat / Sel1-like repeat / Sel1-like repeats. / beta-lactamase activity / beta-lactamase / Tetratricopeptide-like helical domain superfamily / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Sel1 repeat protein
Function and homology information
Biological speciesOxalobacter formigenes OXCC13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.353 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 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sel1 repeat protein
B: Sel1 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,14117
Polymers119,0102
Non-polymers1,13115
Water6,413356
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)213.059, 44.976, 142.734
Angle α, β, γ (deg.)90.000, 92.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-728-

HOH

21B-777-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Sel1 repeat protein


Mass: 59524.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00935 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X9N1, beta-lactamase
#2: Protein Sel1 repeat protein


Mass: 59485.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00935 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X9N1, beta-lactamase

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Non-polymers , 5 types, 371 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Lithium sulfate, Tris-HCl, 20% PEG4000

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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: Jun 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 53054 / % possible obs: 93 % / Redundancy: 4 % / Biso Wilson estimate: 27.47 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.03 / Rrim(I) all: 0.064 / Χ2: 0.762 / Net I/σ(I): 9.4 / Num. measured all: 213350
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.393.10.38516140.8740.2450.4590.84357.9
2.39-2.433.20.33419250.9210.2080.3950.82468.5
2.43-2.483.20.32723750.9370.2010.3860.86582.9
2.48-2.533.40.3226470.9310.1930.3750.81294
2.53-2.593.70.29827320.9460.1760.3470.82796.8
2.59-2.653.80.28627740.9630.1630.330.83197.4
2.65-2.7140.27427350.9620.1510.3140.80597.9
2.71-2.794.10.25827730.9750.1380.2930.83597.3
2.79-2.874.10.21427320.9770.1130.2430.79596.8
2.87-2.964.20.18727200.980.0980.2120.75595.6
2.96-3.074.40.15627510.9880.080.1760.77898.1
3.07-3.194.40.11428070.9910.0590.1290.75798.1
3.19-3.334.30.08727750.9910.0460.0990.75898.2
3.33-3.514.20.06327940.9940.0340.0720.77296.9
3.51-3.734.20.05327440.9940.0290.0610.78996.1
3.73-4.024.40.04627910.9940.0240.0520.77998.5
4.02-4.424.30.03928210.9940.0210.0440.75597.9
4.42-5.064.20.03727700.9940.020.0420.71996.1
5.06-6.374.30.03228740.9940.0170.0370.55898.3
6.37-5040.02929000.9940.0160.0340.55995.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.353→47.519 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.83
RfactorNum. reflection% reflection
Rfree0.2475 2463 5.04 %
Rwork0.1899 --
obs0.1928 48900 74.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.85 Å2 / Biso mean: 40.148 Å2 / Biso min: 8.96 Å2
Refinement stepCycle: final / Resolution: 2.353→47.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8041 0 71 356 8468
Biso mean--66.87 36.4 -
Num. residues----1015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3525-2.37920.3924370.292686490124
2.3792-2.40720.3588590.2579950100928
2.4072-2.43660.3612490.25391100114932
2.4366-2.46740.3249880.24121360144839
2.4674-2.49990.3823730.24861572164545
2.4999-2.53410.2898900.24191780187052
2.5341-2.57030.3669960.24761857195354
2.5703-2.60870.2882960.25132073216958
2.6087-2.64950.32631090.25082180228961
2.6495-2.69290.30921350.2412265240067
2.6929-2.73930.3261460.24982391253770
2.7393-2.78910.35131480.23912500264871
2.7891-2.84280.3411400.24272579271975
2.8428-2.90080.28141350.2512675281077
2.9008-2.96380.33031580.2592931308982
2.9638-3.03280.29881670.23293001316887
3.0328-3.10860.28581980.2233079327790
3.1086-3.19260.31851760.22633188336492
3.1926-3.28660.26911520.21283261341394
3.2866-3.39260.22761530.21443334348795
3.3926-3.51380.24461570.20413273343093
3.5138-3.65450.23511610.19223198335992
3.6545-3.82070.25261480.1733394354298
3.8207-4.02210.23791380.15663434357297
4.0221-4.27390.20512120.13653309352197
4.2739-4.60370.1911740.12733338351295
4.6037-5.06650.14681450.13533329347495
5.0665-5.79850.22092120.15813390360298
5.7985-7.30120.20731550.16073282343794
7.3012-47.5290.18062380.1663256349495
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0258-0.0145-0.01280.0181-0.00750.0257-0.02840.0229-0.0442-0.030.0213-0.00280.04990.01190.09580.1640.03170.02870.156-0.05810.062255.4961-16.480821.6817
20.0655-0.0151-0.01990.02380.01220.00940.0463-0.0378-0.0142-0.08280.0160.05420.0256-0.00750.28190.1040.0258-0.02670.13410.07840.121130.7063-2.229723.8643
30.0438-0.04490.00570.0495-0.00370.0014-0.1358-0.0492-0.0688-0.0188-0.02520.00910.05270.0055-0.95010.25120.0653-0.0101-0.0210.03740.28558.3834-23.792611.3734
40.065-0.05360.07890.2101-0.07510.1142-0.02510.1268-0.0435-0.1072-0.0211-0.0485-0.0762-0.1136-0.15940.16290.01710.02970.2014-0.05290.121-27.6939-29.682813.4271
50.2413-0.2287-0.24220.45160.14330.2847-0.0529-0.19520.0480.21740.2146-0.06940.1031-0.16170.66860.18840.0202-0.09610.28720.06810.1707-46.42189.481346.6706
60.18570.04010.00370.2694-0.03890.18560.0346-0.0632-0.02960.068-0.2106-0.0859-0.0011-0.0261-0.75430.0597-0.0437-0.02550.23520.03980.1619-12.3358-3.781958.5848
70.04160.0187-0.02080.07160.01690.02220.023-0.0849-0.07030.0883-0.0586-0.01240.03430.01180.14250.26330.00010.06140.81850.2640.280126.5168-11.477957.9468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 94 )A15 - 94
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 204 )A95 - 204
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 345 )A205 - 345
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 523 )A346 - 523
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 168 )B16 - 168
6X-RAY DIFFRACTION6chain 'B' and (resid 169 through 345 )B169 - 345
7X-RAY DIFFRACTION7chain 'B' and (resid 346 through 522 )B346 - 522

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