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- PDB-3dns: The N-terminal domain of Ribosomal-protein-alanine acetyltransfer... -

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Basic information

Entry
Database: PDB / ID: 3dns
TitleThe N-terminal domain of Ribosomal-protein-alanine acetyltransferase from Clostridium acetobutylicum ATCC 824
ComponentsRibosomal-protein-alanine acetyltransferase
KeywordsTRANSFERASE / N-terminal domain of Ribosomal-protein-alanine acetyltransferase / MCSG / PSI / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / Ribosomal protein
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal-protein-alanine acetyltransferase (Acetylating enzyme for N-terminal of ribosomal protein S5)
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsNocek, B. / Hendricks, R. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The N-terminal domain of Ribosomal-protein-alanine acetyltransferase from Clostridium acetobutylicum ATCC 824
Authors: Nocek, B. / Hendricks, R. / Cobb, G. / Joachimiak, A.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal-protein-alanine acetyltransferase
B: Ribosomal-protein-alanine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)32,2482
Polymers32,2482
Non-polymers00
Water3,477193
1
A: Ribosomal-protein-alanine acetyltransferase

B: Ribosomal-protein-alanine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)32,2482
Polymers32,2482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565-y,-x+1,-z+1/21
Buried area1850 Å2
ΔGint-9 kcal/mol
Surface area13890 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-4 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.619, 59.619, 196.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsauthors state that the biological unit is Unknown.

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Components

#1: Protein Ribosomal-protein-alanine acetyltransferase / Acetylating enzyme for N-terminal of ribosomal protein S5


Mass: 16123.908 Da / Num. of mol.: 2 / Fragment: residues 1-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CA_C0152 / Plasmid: pmcsg7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97MP0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M NaCl, 0.1 M citrate ph 5.5 40% propanediol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 39476 / Num. obs: 38325 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.296 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.202 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24607 1078 5.1 %RANDOM
Rwork0.19726 ---
all0.19967 20939 --
obs0.19967 19861 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.555 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2--1.28 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 0 193 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222189
X-RAY DIFFRACTIONr_bond_other_d0.0010.021544
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.9642927
X-RAY DIFFRACTIONr_angle_other_deg0.94233774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5665258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59425.094106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31115445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.828158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_nbd_refined0.2180.2374
X-RAY DIFFRACTIONr_nbd_other0.1990.21579
X-RAY DIFFRACTIONr_nbtor_refined0.190.21049
X-RAY DIFFRACTIONr_nbtor_other0.0890.21221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0741.51603
X-RAY DIFFRACTIONr_mcbond_other0.2481.5532
X-RAY DIFFRACTIONr_mcangle_it1.31622091
X-RAY DIFFRACTIONr_scbond_it2.03131045
X-RAY DIFFRACTIONr_scangle_it2.7584.5836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 81 -
Rwork0.17 1463 -
obs--98.85 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.7216-7.42230.830919.0676-6.3535.35580.426-0.30310.41511.3359-0.2189-0.5390.472-0.2941-0.20710.1643-0.1024-0.0670.253-0.0114-0.002127.027712.697972.0885
211.99218.71733.75845.37426.34521.19190.4124-0.75250.56931.773-0.43850.58870.2854-0.12850.02610.1848-0.05260.04530.2026-0.03660.047423.93115.963169.6355
313.8106-6.0993-7.327919.858314.522511.3092-0.07860.1661-1.44960.9088-0.70520.38441.6237-1.25220.78380.2147-0.08330.11340.1765-0.01050.184418.41152.259362.1709
43.1028-1.4741-4.88147.2744.64098.4996-0.4327-0.330.05120.2740.116-0.02910.3277-0.06570.31670.1082-0.00930.02030.18410.02270.070520.603410.659863.2746
58.9715.63873.891715.199311.290512.09240.2031-0.55240.10220.3020.0048-0.144-0.4953-0.1558-0.20780.20440.0287-0.02360.1851-0.01970.052417.763320.822669.5586
64.4585-4.3144-1.17346.35412.66933.785-0.1113-0.0749-0.1284-0.07450.15490.0982-0.0485-0.0114-0.04360.104-0.06580.06870.13920.00230.091623.87377.962657.1127
75.4392-3.6478-0.71953.0483-0.05471.05360.026-0.1102-0.1630.0106-0.01750.13250.185-0.0883-0.00850.1776-0.0340.03830.13840.02690.089733.42381.17855.5106
88.5972-7.1043-0.706715.81386.70753.8293-0.27430.20890.3381-0.0967-0.2049-0.0777-0.08840.08670.47920.1326-0.05020.02630.16260.05390.04120.662521.829256.4854
913.7221-8.06512.276119.8891-7.458116.4443-0.1177-0.39130.56360.5089-0.18810.1151-0.3597-0.31930.30580.0645-0.03-0.02060.0714-0.03140.159727.875124.754562.3853
105.0452-2.7886-0.83112.7429-3.68467.7270.0899-0.29060.50170.0221-0.1311-0.22820.25140.05270.04120.1152-0.06770.02420.1692-0.00770.117131.635817.318864.5704
110.8977-0.6527-2.30512.84160.88496.1834-0.0103-0.1535-0.11560.295-0.2294-0.08330.17840.26690.23970.1712-0.0479-0.00040.16840.04210.063535.77345.547464.5382
120.2619-1.41880.4729.2796-2.99680.9721-0.28530.34370.38040.3787-0.1948-0.37630.05580.04060.480.1364-0.0190.03410.16380.03730.113533.97958.749253.7175
139.4868-3.06645.666319.23997.995818.3181-0.2057-0.13240.2469-0.6124-0.06010.3756-0.87090.23870.26580.124-0.04140.05040.11870.04860.08526.663120.536249.8944
1415.77325.5022-3.796910.4403-8.717521.79590.6138-0.89621.032-0.4496-0.11110.4285-0.39750.1669-0.50270.0686-0.07640.02780.0922-0.0370.107136.406320.711656.5456
159.68220.59432.74422.86170.57360.83590.08260.33950.2621-0.3042-0.1007-0.0411-0.27010.05280.01810.14330.02430.07510.2040.03050.029529.600214.281743.6998
1654.43579.9732-13.38520.78569.763323.4264-0.66060.80853.518-0.4016-0.09331.3547-1.8077-0.69480.75380.19150.1365-0.10420.21140.04990.283616.017819.398841.118
1714.0604-4.189.71763.9469-3.23726.7610.07570.29410.2394-0.0182-0.1834-0.1403-0.37620.09990.10770.11820.01140.09050.14590.04750.049232.418214.413749.2213
1817.01725.79441.375824.3116.093815.86560.19950.27610.34030.25830.0989-1.57330.69531.077-0.29840.01910.0034-0.07010.21850.02720.094244.36569.837462.4494
1920.3147-21.4872-13.242323.039316.097722.65120.08781.90710.5551-0.5146-1.0430.298-0.2022-2.57020.95520.08260.0071-0.12230.3198-0.10190.175526.8041-11.716325.6697
2010.97210.7539-1.56129.49340.70757.27920.4006-0.3504-0.30270.98350.14160.87870.8867-1.0391-0.54220.15230.003-0.04160.1402-0.1310.268722.6978-13.153640.0538
214.8367-1.0959-5.99775.86532.246916.6675-0.04060.226-0.33040.3841-0.26690.67230.4278-0.0630.30750.0373-0.0770.07360.0938-0.08890.145525.8489-10.383340.6235
225.444-0.7147-2.396410.81211.57834.19570.17360.5632-0.4524-0.5570.28850.3390.43050.451-0.46210.1166-0.0062-0.01480.1611-0.08250.181532.3639-18.854731.0261
231.03610.5127-0.94660.2608-0.37921.9925-0.18150.1281-0.13550.45570.09970.12380.1730.11260.08180.14770.00480.02810.1327-0.01820.112127.5956-5.322843.0686
245.8439-5.2788-0.07245.9359-0.30250.54470.11590.1768-0.3374-0.0253-0.2010.3544-0.1565-0.1030.08510.10210.00650.02290.2035-0.03550.08722.54484.055642.2832
2512.9167-9.7408-3.55038.40560.45695.6280.2472-0.93390.13710.3126-0.2694-0.0874-0.0530.21620.02220.1982-0.031-0.01030.1345-0.02250.082739.47-10.539339.4801
267.7541-7.82654.72369.3226-8.514512.74240.35850.41530.0874-0.5114-0.582-0.55050.1561-0.2010.22350.2220.04430.04560.13540.05590.062641.5545-9.102628.8296
273.4043-2.8569-1.0829.54215.59623.42020.97770.5-0.1235-0.7871-0.84210.21650.4360.1663-0.13550.16640.07860.02660.2118-0.02240.053833.3527-6.980928.4463
281.4-2.24072.38733.7596-3.69964.15540.32710.39160.1049-0.4246-0.27930.4156-0.1195-0.342-0.04780.11280.0555-0.00040.2886-0.07190.055326.3731-2.756431.6597
296.0142-4.1842-7.063411.6075-3.423616.28960.27710.3522-0.2884-1.2619-0.73110.7864-0.0212-0.58780.4540.07880.0226-0.02830.3147-0.1340.031419.755-0.098831.7634
301.43560.0151-0.75411.06650.45761.34580.04860.3052-0.0064-0.0503-0.25820.13660.0891-0.04660.20950.11270.01970.02270.2115-0.05340.091123.00214.160937.4506
311.9710.59371.32760.1820.11326.47910.2441-0.05690.0605-0.1162-0.2386-0.28850.30810.7349-0.00550.15410.04740.04080.15230.06030.11341.2429-1.189536.9966
322.4745-3.0147-4.27713.556.10967.47420.4932-0.04430.16760.1017-0.02510.0395-0.220.4688-0.4680.17330.08310.01420.26540.03390.006735.57544.970331.3121
330.5926-1.41942.50739.0262-5.14410.7395-0.1133-0.10270.06480.1225-0.3083-0.7365-0.37340.30440.42160.0490.00580.03940.19940.08310.13439.87214.337547.7061
3413.9387-6.48010.360146.6479-11.190718.06540.3214-0.1136-0.77340.4793-0.5671-0.07051.1031.47980.24570.12110.12980.03020.18960.05850.137345.9408-4.627351.4374
358.9281-4.2438.70733.0273-4.13789.36660.08180.39290.07340.0267-0.1925-0.2561-0.37010.23180.11070.11690.0130.0830.14840.00610.069734.8645.295239.2207
368.67587.1886-2.97037.37492.140415.94370.43161.68671.0193-1.5506-0.31470.2378-0.3252-0.7749-0.1170.1880.1517-0.0610.2457-0.0233023.12868.628527.8129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 53 - 8
2X-RAY DIFFRACTION2AA6 - 109 - 13
3X-RAY DIFFRACTION3AA11 - 1714 - 20
4X-RAY DIFFRACTION4AA18 - 2221 - 25
5X-RAY DIFFRACTION5AA23 - 2826 - 31
6X-RAY DIFFRACTION6AA29 - 3732 - 40
7X-RAY DIFFRACTION7AA38 - 4741 - 50
8X-RAY DIFFRACTION8AA48 - 5551 - 58
9X-RAY DIFFRACTION9AA56 - 6159 - 64
10X-RAY DIFFRACTION10AA62 - 6765 - 70
11X-RAY DIFFRACTION11AA68 - 7971 - 82
12X-RAY DIFFRACTION12AA80 - 8483 - 87
13X-RAY DIFFRACTION13AA85 - 9088 - 93
14X-RAY DIFFRACTION14AA91 - 9994 - 102
15X-RAY DIFFRACTION15AA100 - 110103 - 113
16X-RAY DIFFRACTION16AA111 - 115114 - 118
17X-RAY DIFFRACTION17AA116 - 124119 - 127
18X-RAY DIFFRACTION18AA125 - 129128 - 132
19X-RAY DIFFRACTION19BB2 - 65 - 9
20X-RAY DIFFRACTION20BB7 - 1610 - 19
21X-RAY DIFFRACTION21BB17 - 2220 - 25
22X-RAY DIFFRACTION22BB23 - 2826 - 31
23X-RAY DIFFRACTION23BB29 - 3732 - 40
24X-RAY DIFFRACTION24BB38 - 4841 - 51
25X-RAY DIFFRACTION25BB49 - 5352 - 56
26X-RAY DIFFRACTION26BB54 - 5957 - 62
27X-RAY DIFFRACTION27BB60 - 6463 - 67
28X-RAY DIFFRACTION28BB65 - 6968 - 72
29X-RAY DIFFRACTION29BB70 - 7473 - 77
30X-RAY DIFFRACTION30BB75 - 8478 - 87
31X-RAY DIFFRACTION31BB85 - 9388 - 96
32X-RAY DIFFRACTION32BB94 - 10197 - 104
33X-RAY DIFFRACTION33BB102 - 110105 - 113
34X-RAY DIFFRACTION34BB111 - 116114 - 119
35X-RAY DIFFRACTION35BB117 - 124120 - 127
36X-RAY DIFFRACTION36BB125 - 129128 - 132

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