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- PDB-3jwp: Crystal structure of Plasmodium falciparum SIR2A (PF13_0152) in c... -

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Basic information

Entry
Database: PDB / ID: 3jwp
TitleCrystal structure of Plasmodium falciparum SIR2A (PF13_0152) in complex with AMP
ComponentsTranscriptional regulatory protein sir2 homologue
KeywordsTRANSCRIPTION / malaria / transcription regulation / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent histone deacetylase activity / chromatin silencing complex / telomere capping / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transferase activity / chromosome, telomeric region / nucleolus ...protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent histone deacetylase activity / chromatin silencing complex / telomere capping / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transferase activity / chromosome, telomeric region / nucleolus / regulation of DNA-templated transcription / mitochondrion / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / TRIETHYLENE GLYCOL / NAD-dependent protein deacylase Sir2A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Lin, Y.H. / MacKenzie, F. / Senisterra, G. / Allali-Hassanali, A. / Vedadi, M. / Ravichandran, M. / Cossar, D. / Kozieradzki, I. ...Wernimont, A.K. / Hutchinson, A. / Lin, Y.H. / MacKenzie, F. / Senisterra, G. / Allali-Hassanali, A. / Vedadi, M. / Ravichandran, M. / Cossar, D. / Kozieradzki, I. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Qiu, W. / Brand, V. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Plasmodium falciparum SIR2A (PF13_0152) in complex with AMP
Authors: Wernimont, A.K. / Hutchinson, A. / Lin, Y.H. / MacKenzie, F. / Senisterra, G. / Allali-Hassanali, A. / Vedadi, M. / Ravichandran, M. / Cossar, D. / Kozieradzki, I. / Zhao, Y. / Schapira, M. ...Authors: Wernimont, A.K. / Hutchinson, A. / Lin, Y.H. / MacKenzie, F. / Senisterra, G. / Allali-Hassanali, A. / Vedadi, M. / Ravichandran, M. / Cossar, D. / Kozieradzki, I. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Qiu, W. / Brand, V.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein sir2 homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1874
Polymers29,6241
Non-polymers5633
Water543
1
A: Transcriptional regulatory protein sir2 homologue
hetero molecules

A: Transcriptional regulatory protein sir2 homologue
hetero molecules

A: Transcriptional regulatory protein sir2 homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,56012
Polymers88,8713
Non-polymers1,6889
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area8410 Å2
ΔGint-55 kcal/mol
Surface area29600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.564, 106.564, 44.968
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Transcriptional regulatory protein sir2 homologue


Mass: 29623.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF13_0152, Sir2 / Plasmid: pet15MLH / Production host: Escherichia coli (E. coli) / Strain (production host): Pet15 / References: UniProt: Q8IE47
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growDetails: 17 % PEG 3350, 0.1 M NaCitrate pH 5.7, 0.1 mM beta-OG, 2.6 mM AMP, 2.6 mM peptide(SGRGKacGGKacGLGKacGGAKacRHR)

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.978
SYNCHROTRONCHESS A120.978
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMay 1, 2009
ADSC QUANTUM 2102CCDMay 1, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionRedundancy: 14.9 % / Av σ(I) over netI: 32.77 / Number: 131157 / Rmerge(I) obs: 0.064 / Χ2: 1.39 / D res high: 2.63 Å / D res low: 50 Å / Num. obs: 8831 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.135099.210.0481.3714.7
5.667.1310010.0561.74215.6
4.955.6610010.0561.41915.9
4.54.9510010.0541.5516
4.174.510010.0532.16616
3.934.1710010.0582.3616.2
3.733.9310010.0662.04116.1
3.573.7310010.081.68216.2
3.433.5710010.0871.53816.3
3.313.4310010.1091.24616.1
3.213.3110010.1371.19416.1
3.123.2110010.1681.16716.3
3.043.1210010.2291.02816.2
2.963.0410010.2871.02316.3
2.892.9610010.4470.97815.9
2.832.8910010.5250.91914.1
2.782.8310010.5890.91313.3
2.722.7810010.7410.86712
2.682.7299.810.8439.9
2.632.689210.8617.1
ReflectionResolution: 2.65→50 Å / Num. all: 10263 / Num. obs: 10243 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 81.3 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.078 / Χ2: 1.932 / Net I/σ(I): 8.9
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 2.05 / Num. unique all: 410 / Rsym value: 0.914 / Χ2: 1.283 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
Adxvdata processing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→34.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.79 / SU B: 28.57 / SU ML: 0.294 / SU R Cruickshank DPI: 1.115 / SU Rfree: 0.36 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.115 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.274 406 4.7 %RANDOM
Rwork0.206 ---
all0.209 8666 --
obs0.209 8584 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.27 Å2 / Biso mean: 33.138 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.65→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 34 3 1925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221958
X-RAY DIFFRACTIONr_bond_other_d0.0010.021222
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9662670
X-RAY DIFFRACTIONr_angle_other_deg0.8143.0013010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06925.65269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00115306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.986152
X-RAY DIFFRACTIONr_chiral_restr0.0570.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_mcbond_it0.2851.51266
X-RAY DIFFRACTIONr_mcbond_other0.0411.5517
X-RAY DIFFRACTIONr_mcangle_it0.53822038
X-RAY DIFFRACTIONr_scbond_it0.7983692
X-RAY DIFFRACTIONr_scangle_it1.3044.5632
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 33 -
Rwork0.29 582 -
all-615 -
obs-582 97.77 %
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)
15.1401-1.2886-0.25054.95071.63565.21810.07170.3141-0.7747-0.5002-0.106-0.4740.53990.29640.03430.3820.06410.11510.1997-0.04310.4113-35.7149.549-27.4797
27.29131.31450.88928.06220.60722.96630.5843-1.0524-0.20550.2846-0.59750.22410.0784-0.04720.01320.2022-0.10560.02860.4877-0.0110.1942-41.072927.4003-2.9355
33.6555-2.1811.79338.522110.32258.57930.1096-0.4142-0.21330.2480.7843-1.15940.05571.249-0.89390.4979-0.15350.1150.5060.1150.6842-26.158319.2492-13.6769
45.2706-1.68340.50595.82252.23997.9474-0.23390.063-0.0886-0.20230.3-0.8524-0.02740.1754-0.06620.2317-0.04880.08310.21510.07330.3664-31.450624.6831-20.5978
55.14882.34770.43484.23010.05150.69590.2743-0.2127-0.28870.1426-0.5077-0.14460.13010.0640.23340.2431-0.05390.01480.4287-0.02380.2671-31.505738.5751-6.6726
65.4909-0.13831.64894.69580.01735.40670.02240.353-0.011-0.46020.0473-0.2605-0.2804-0.3713-0.06980.2883-0.01140.09790.23440.06060.1984-43.026121.4643-27.5639
76.8091-0.5810.71845.272-1.04396.0772-0.1231-0.2012-1.0037-0.46020.1701-0.15730.8088-0.043-0.0470.524-0.04640.05520.1695-0.04250.4648-36.7997.6769-23.8438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 34
2X-RAY DIFFRACTION2A35 - 72
3X-RAY DIFFRACTION3A73 - 97
4X-RAY DIFFRACTION4A98 - 128
5X-RAY DIFFRACTION5A129 - 174
6X-RAY DIFFRACTION6A175 - 222
7X-RAY DIFFRACTION7A223 - 258

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