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

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Basic information

Entry
Database: PDB / ID: 6orc
TitleCrystal structure of Sel1 repeat protein from Oxalobacter formigenes
ComponentsSel1 repeat protein
KeywordsUNKNOWN FUNCTION / Sel1 repeat / Structural Genomics / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / 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: 2.98 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 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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


Theoretical massNumber of molelcules
Total (without water)30,7832
Polymers30,7832
Non-polymers00
Water1086
1
A: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)15,3921
Polymers15,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)15,3921
Polymers15,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.301, 75.479, 78.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAs per the authors the biological assembly is unknown

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Components

#1: Protein Sel1 repeat protein


Mass: 15391.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00634 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X8T0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl, 20 % PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. obs: 9035 / % possible obs: 99.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.053 / Rrim(I) all: 0.125 / Χ2: 0.848 / Net I/σ(I): 11.7 / Num. measured all: 51377
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.97-3.024.40.9594220.6410.4961.0850.84998.6
3.02-3.084.60.8944480.7040.451.0060.8499.1
3.08-3.144.90.6724400.8120.3290.7510.85599.8
3.14-3.25.90.5034400.8980.2230.5510.876100
3.2-3.2760.3954370.8780.1740.4320.813100
3.27-3.3460.324600.9450.1410.3510.9100
3.34-3.4360.2584390.9640.1150.2830.94399.8
3.43-3.5260.2184480.9640.0980.240.93399.3
3.52-3.6260.1794340.9720.080.1960.91299.8
3.62-3.745.80.1594450.9740.0710.1740.88599.1
3.74-3.885.30.1314630.9710.060.1450.83199.8
3.88-4.036.20.1324420.9740.0570.1440.851100
4.03-4.216.10.1234430.9850.0530.1340.811100
4.21-4.4460.1194680.9730.0530.130.819100
4.44-4.7160.1234450.9780.0530.1340.85799.6
4.71-5.085.50.1164590.980.0520.1270.78799.8
5.08-5.596.20.114640.980.0480.1210.826100
5.59-6.396.10.1164630.9750.0510.1270.813100
6.39-8.055.50.0984720.9740.0450.1090.71798.1
8.05-505.10.1015030.9390.0510.1140.83496.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.98→43.662 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.89
RfactorNum. reflection% reflection
Rfree0.2476 450 5.63 %
Rwork0.2077 --
obs0.2101 8065 82.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.86 Å2 / Biso mean: 58.356 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 2.98→43.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 6 2098
Biso mean---29.74 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9799-3.16650.3438370.330867571225
3.1665-3.41090.32591350.25741987212275
3.4109-3.7540.30051670.22372648281598
3.754-4.29680.251870.18412741282899
4.2968-5.41190.21512080.189826322840100
5.4119-43.66620.2171610.2012636279798
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)
12.36221.49040.26972.48470.66431.47260.0473-0.28580.19440.3514-0.1898-0.1886-0.37070.30540.05090.2124-0.0145-0.02390.2938-0.02780.19614.178425.116672.3682
24.07220.38291.83681.3725-0.24052.31770.11880.2451-0.0204-0.1066-0.1526-0.19120.02170.22940.06680.25480.2455-0.0090.33820.05130.155312.985621.838762.0344
31.2974-0.6290.02473.5106-2.32763.38610.00960.11470.1811-0.0774-0.1012-0.0298-0.3069-0.05150.16230.23240.1401-0.140.3177-0.01050.29483.413525.802458.8385
41.70420.8311-0.72892.37860.04912.03920.08140.15660.0076-0.26670.30720.0362-0.0477-0.17920.03990.39350.0676-0.17320.30570.06190.32671.626823.938952.7501
50.2864-0.19560.14760.295-0.23731.22050.03640.14240.0474-0.15770.05030.2737-0.0819-0.2853-0.00670.51140.2814-0.14520.9940.41360.8251-11.489525.738953.357
60.1199-0.220.10360.413-0.19480.09170.0092-0.0231-0.0381-0.03090.06140.26150.1021-0.2338-0.07210.78190.41660.06171.0080.26221.1279-17.096532.745958.7556
72.40531.19740.77431.88440.48391.7402-0.22540.379-0.246-0.31170.05530.14170.2613-0.18250.07360.4430.0359-0.03460.2345-0.0760.1929-5.46333.894864.2071
80.70270.0056-0.23990.8544-0.23640.93570.0653-0.20630.3330.10240.04140.1998-0.11420.0031-0.01920.32690.24150.03710.3074-0.11610.3302-5.916716.142880.2315
90.166-0.3935-0.05930.93280.05281.0929-0.0004-0.12260.08220.03920.05550.1922-0.2153-0.16330.01810.62430.2560.11710.45-0.1840.9759-11.160432.5581.8783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 37 )A3 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 51 )A38 - 51
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 66 )A52 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 87 )A67 - 87
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 122 )A88 - 122
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 135 )A123 - 135
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 37 )B1 - 37
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 102 )B38 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 134 )B103 - 134

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