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- PDB-4l7m: Crystal structure of the archaeal HEAT-like repeats protein TON_1... -

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Basic information

Entry
Database: PDB / ID: 4l7m
TitleCrystal structure of the archaeal HEAT-like repeats protein TON_1937 from Thermococcus onnurineus NA1
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / HEAT-repeats / Hypothetical
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / HEAT repeat domain-containing protein
Function and homology information
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsKim, Y.G. / Jeong, J.H.
CitationJournal: To be Published
Title: Crystal structure of the archaeal HEAT-like repeats protein TON_1937 from Thermococcus onnurineus NA1
Authors: Kim, Y.G. / Jeong, J.H.
History
DepositionJun 14, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 10, 2013ID: 3B2A
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0214
Polymers60,8362
Non-polymers1842
Water1,17165
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)30,4181
Polymers30,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6023
Polymers30,4181
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.911, 42.445, 77.215
Angle α, β, γ (deg.)90.00, 107.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative uncharacterized protein / TON_1937


Mass: 30418.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: Thermococcus Onnurineus, TON_1937 / Plasmid: pProExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: B6YW62
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-HCl, pH 8.0, 0.8M ammonium acetate, 8% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2011 / Details: mirrors
RadiationMonochromator: a silicon double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 38857 / % possible obs: 93.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 6.4 / Redundancy: 4.3 % / Biso Wilson estimate: 32.23 Å2 / Rsym value: 0.037 / Net I/σ(I): 26.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.211 / % possible all: 85.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.002→28.5 Å / SU ML: 0.25 / σ(F): 1.54 / Phase error: 24.92 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 3720 5.27 %Random
Rwork0.2018 ---
obs0.2036 38857 93.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 12 65 4183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084172
X-RAY DIFFRACTIONf_angle_d1.0755636
X-RAY DIFFRACTIONf_dihedral_angle_d14.271600
X-RAY DIFFRACTIONf_chiral_restr0.066704
X-RAY DIFFRACTIONf_plane_restr0.004702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0023-2.02760.32771250.2644216582
2.0276-2.05430.30391220.258227088
2.0543-2.08240.27061230.2452231188
2.0824-2.11220.33811300.246238988
2.1122-2.14370.27621290.2377234790
2.1437-2.17720.27031300.2359234391
2.1772-2.21290.2541390.2232244391
2.2129-2.2510.26481390.2206249393
2.251-2.29190.24641350.2373239593
2.2919-2.3360.29851410.2133249493
2.336-2.38360.2391340.2069248994
2.3836-2.43540.27471350.2066245894
2.4354-2.49210.23041400.2147255295
2.4921-2.55440.2331410.2061246196
2.5544-2.62340.25231430.2106253496
2.6234-2.70050.24541340.2311253796
2.7005-2.78760.27391450.2316256397
2.7876-2.88710.27021430.2209250797
2.8871-3.00260.28591430.2405256897
3.0026-3.13910.31091440.2486259197
3.1391-3.30440.27351380.2219256197
3.3044-3.51110.2291510.2204259397
3.5111-3.78160.231420.1953255498
3.7816-4.16110.21861430.1727257898
4.1611-4.76080.17961470.1472259598
4.7608-5.98890.18271460.187260598
5.9889-28.50330.17131380.1548245493
Refinement TLS params.Method: refined / Origin x: -23.9389 Å / Origin y: 8.9465 Å / Origin z: -0.205 Å
111213212223313233
T0.1938 Å2-0.0019 Å2-0.0186 Å2-0.2086 Å2-0.0124 Å2--0.2112 Å2
L0.2555 °2-0.0034 °2-0.1383 °2-0.265 °2-0.1829 °2--0.568 °2
S-0.0208 Å °-0.0517 Å °0.0472 Å °0.0298 Å °0.0298 Å °0.0271 Å °-0.043 Å °-0.0348 Å °-0.0167 Å °
Refinement TLS groupSelection details: ALL

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