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- PDB-3h0k: Crystal structure of an adenylated kinase related protein from su... -

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Basic information

Entry
Database: PDB / ID: 3h0k
TitleCrystal structure of an adenylated kinase related protein from sulfolobus solfataricus to 3.25a
ComponentsUPF0200 protein SSO1041
Keywordsstructural genomics / unknown function / ADENYLATE / KINASE / SULFOLOBUS / SOLFATARICUS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / ATP-binding / Nucleotide-binding
Function / homologyNucleoside triphosphate hydrolase-related / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / ATP binding / Alpha Beta / UPF0200 protein SSO1041
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å
AuthorsStein, A.J. / Sather, A. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of an adenylated kinase related protein from sulfolobus solfataricus to 3.25a
Authors: Stein, A.J. / Sather, A. / Abdullah, J. / Joachimiak, A.
History
DepositionApr 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: UPF0200 protein SSO1041
B: UPF0200 protein SSO1041
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0784
Polymers40,8852
Non-polymers1922
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-43 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.418, 65.418, 205.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein UPF0200 protein SSO1041


Mass: 20442.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: SSO1041 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97Z90
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.69 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.26M AMMONIUM SULFATE, 0.1M CACODYLATE PH 6.5, VAPOR DIFFUSION, TEMPERATURE 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2009
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 8509 / % possible obs: 97.7 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 5.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.923 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.25→47.3 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.883 / SU B: 59.755 / SU ML: 0.445 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.576 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.294 354 4.7 %RANDOM
Rwork0.221 ---
obs0.225 7566 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.25→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 10 10 2536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222552
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9893452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64423.26395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.07215428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3681519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021853
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4091.51678
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78822663
X-RAY DIFFRACTIONr_scbond_it1.1823874
X-RAY DIFFRACTIONr_scangle_it2.1194.5789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 24 -
Rwork0.262 508 -
obs--98.89 %
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)
11.82351.29361.46861.31420.50111.9691-0.07490.08660.18920.18690.01780.1931-0.37390.28470.05710.39410.02620.02080.42250.02140.3621-22.061717.8608-9.3857
23.80463.03491.71547.0438-0.12662.1575-0.30680.05530.55160.23580.1893-0.1243-0.83790.57950.11750.5493-0.2410.07740.5611-0.10540.4475-16.987425.3351-9.4128
32.99510.99961.23391.09122.37526.8572-0.0038-0.21240.46060.10250.0795-0.0256-0.62170.6253-0.07560.6799-0.1154-0.05930.5021-0.03880.4297-17.341324.4193-2.1043
47.03350.8187-0.47576.77952.35444.44340.2135-0.5232-0.25241.02410.1934-1.00930.61251.4579-0.40690.62120.1283-0.23880.7948-0.03690.414-8.965110.70893.6257
54.7173-2.69510.94434.61620.10360.40620.3831.37120.0841-0.809-0.79130.269-0.1180.04810.40840.50280.1121-0.10820.9087-0.15790.5875-5.99573.07540.0706
63.2099-0.75941.86665.56961.82287.16110.3868-0.082-0.60.87440.1206-0.70631.21630.8871-0.50740.93580.1896-0.22040.63750.08910.5387-15.64770.94140.9496
74.3153-1.5779-1.40662.7074-2.46564.7915-0.2754-0.63740.00620.39390.2269-0.10450.0460.29770.04850.83190.0658-0.1340.55430.02740.3409-20.603711.03755.438
80.45920.22931.02694.49490.26094.5643-0.0325-0.45120.3061.0084-0.0470.2719-0.6019-0.27050.07950.8267-0.06330.07480.8741-0.28880.6205-22.408924.19538.1429
93.61670.12420.43240.30011.44347.11890.129-0.15010.13070.0472-0.0104-0.018-0.03580.3842-0.11860.4832-0.01920.03360.40220.06830.3282-22.665215.4558-3.7989
104.9395-4.27982.22046.58321.24595.5983-0.0934-0.2879-0.57611.0750.00810.29370.8674-0.36870.08530.5831-0.02710.03350.42540.08110.4299-28.287411.22430.0917
111.17390.87261.47163.26940.96074.85870.1405-0.11820.32070.2915-0.09330.4181-0.6491-0.4489-0.04720.35320.03840.04820.38860.04090.3109-27.367717.0014-7.217
127.43431.46812.38848.4611.75218.5381-0.33510.73160.0505-0.42010.6637-0.4826-0.66021.4847-0.32860.3354-0.14370.07160.8181-0.03850.3938-12.611614.2603-23.9447
139.54515.55483.47594.27082.55042.7049-0.11270.4081-0.10030.17380.6746-0.9806-0.58441.6751-0.56190.6547-0.4704-0.03931.7605-0.34270.9092-3.30615.9735-18.839
149.68533.60922.76956.64452.94654.2127-0.03890.7789-0.8068-0.03370.7275-1.81350.21932.3467-0.68860.5060.14010.01971.5287-0.1920.8213-7.01715.4854-21.4401
1513.67794.0967-3.337811.915-2.469713.43470.17910.2414-1.35950.50290.4679-0.79410.9641.6262-0.6470.55890.1869-0.06440.7797-0.10110.6445-13.73222.7224-16.147
167.7681-1.07851.32576.44680.75927.23180.0535-0.1397-0.57090.5490.1133-0.12240.7230.4535-0.16680.4640.04010.00710.47710.04420.4248-23.64316.522-12.1595
174.22613.2030.29678.7311-0.45845.3253-0.041-0.04590.75740.1868-0.07190.5758-0.8694-0.21160.11280.46060.0577-0.01160.44770.07590.4929-29.412618.9799-14.352
182.13890.51571.6281.24440.92518.3438-0.68150.83361.1284-0.9120.6709-0.1483-2.1041.7490.01061.1272-0.4728-0.00050.96690.15290.8231-17.363425.6028-22.6425
196.7610.5531-1.3692.551.54986.2574-0.43990.64890.8764-0.80640.31090.204-1.56880.6810.1290.8619-0.1944-0.07580.46780.1750.5942-21.193730.0926-19.5578
202.80781.31910.55564.45161.74934.9615-0.2154-0.36851.01990.0901-0.20711.021-1.4282-0.42330.42250.83680.0975-0.04270.45790.00880.8036-29.35330.0805-10.6172
211.6035-0.6668-4.04120.39771.520915.12590.11510.2372-0.0109-0.2429-0.07580.0752-0.71670.6334-0.03930.4277-0.1341-0.06060.60250.06520.2705-28.96338.788-35.1214
224.64990.20912.92731.64121.60377.673-0.24170.45460.4136-0.2988-0.13430.7066-0.3361-0.82490.3760.29730.0308-0.03660.54550.06190.5079-38.57811.3855-23.3418
234.70461.64740.16484.38652.04136.323-0.39280.52570.5785-0.65270.08690.7004-1.0142-0.61020.30590.52730.0206-0.24870.70010.17140.4755-39.574915.477-35.6434
243.4265-0.05591.41444.09693.91334.3703-0.14240.4017-0.0202-0.222-0.27990.3426-0.3097-0.24420.42230.2686-0.1036-0.14190.69320.040.3115-38.50155.1149-35.4622
256.3009-0.93282.71916.1144-2.72064.8455-0.07280.5905-0.26870.0165-0.08190.67610.6036-1.06930.15470.4833-0.2413-0.02640.7952-0.12250.5788-42.6679-4.8236-31.104
261.04990.9815-1.24450.9956-0.88674.2131-0.63540.5861-0.0905-0.64590.7589-0.27950.54050.435-0.12350.6628-0.40110.04250.8789-0.18890.657-46.0383-13.086-27.2513
275.1761-0.2089-0.43331.00612.2637.41050.2046-0.0209-0.420.5897-0.23580.4351.3325-1.06880.03120.7577-0.2730.07030.63630.00550.7305-40.865-8.6699-20.9563
285.22361.11261.80035.05050.77433.84310.11790.238-0.86540.42350.0941-0.1761.29950.001-0.21190.6656-0.0745-0.020.4393-0.09450.5563-32.1524-10.3211-25.6551
293.94511.77020.59713.909-0.00258.6309-0.15341.1692-0.382-0.65310.24430.24520.6876-0.1929-0.0910.4505-0.1251-0.02830.6662-0.13930.3913-33.7882-4.5011-36.7482
302.56571.90311.78313.7914-0.69944.5897-0.2730.88020.027-0.70370.27240.25240.23440.09370.00060.4376-0.022-0.03270.8214-0.01060.3903-31.63043.4831-35.3243
313.5536-0.138-1.91464.21523.33089.691-0.17350.829-0.7959-0.11190.4165-0.20660.72910.4401-0.2430.39960.00180.00530.6294-0.10910.4109-25.1359-1.4593-31.0438
322.02832.34590.68774.5038-1.53644.7386-0.32250.818-0.0257-0.61690.4809-0.2857-0.46860.6426-0.15850.4816-0.0180.13310.81550.03090.4336-24.81086.6837-33.7641
334.28260.26431.26073.04981.28435.1596-0.1671-0.16360.42710.0868-0.16010.7274-0.3826-0.82570.32720.34910.09260.02420.50940.03340.551-37.753615.7511-15.1999
343.6312-4.03063.36246.6354-1.03317.3054-0.1291-0.23030.3657-0.24-0.4380.4486-0.4302-1.27840.56710.36150.07730.01320.8183-0.0431.0689-46.737314.4937-14.5236
351.21691.07440.76821.00461.04356.65540.2429-0.54240.49010.3783-0.59780.57630.5688-1.82260.35490.464-0.14240.2950.8659-0.04980.8005-45.7026.2719-8.5269
3614.38053.7835-5.203715.2214-2.427511.98040.1805-0.530.18830.6084-0.19580.58350.6255-0.80760.01530.4605-0.11030.13020.580.00630.5008-39.76643.3082-10.7921
373.5465-4.36920.66626.50390.35621.39930.08210.0523-0.69360.4561-0.15580.90230.3834-0.39950.07370.4761-0.10350.03990.61330.04490.4689-34.05280.469-15.3212
386.050.57140.44323.25561.10365.8534-0.24270.38190.286-0.13880.21650.2187-0.3832-0.02720.02620.3166-0.0173-0.01110.42120.07970.3281-28.543212.8589-22.3366
393.92840.1179-0.78562.81981.25955.3092-0.5680.63120.8965-0.80070.00240.7407-1.3221-0.51080.56560.9120.1411-0.25520.73150.20890.8729-37.44724.6058-27.7978
408.06090.7535-8.11811.22480.811410.33160.02970.8870.5021-0.91050.62840.1237-1.46380.2312-0.65811.0003-0.292-0.03331.01630.20570.5444-27.34419.655-35.1548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 20
2X-RAY DIFFRACTION2A21 - 29
3X-RAY DIFFRACTION3A30 - 39
4X-RAY DIFFRACTION4A40 - 48
5X-RAY DIFFRACTION5A49 - 56
6X-RAY DIFFRACTION6A57 - 70
7X-RAY DIFFRACTION7A71 - 78
8X-RAY DIFFRACTION8A79 - 86
9X-RAY DIFFRACTION9A87 - 97
10X-RAY DIFFRACTION10A98 - 103
11X-RAY DIFFRACTION11A104 - 119
12X-RAY DIFFRACTION12A120 - 125
13X-RAY DIFFRACTION13A126 - 130
14X-RAY DIFFRACTION14A135 - 142
15X-RAY DIFFRACTION15A143 - 147
16X-RAY DIFFRACTION16A148 - 158
17X-RAY DIFFRACTION17A159 - 165
18X-RAY DIFFRACTION18A166 - 170
19X-RAY DIFFRACTION19A171 - 176
20X-RAY DIFFRACTION20A177 - 185
21X-RAY DIFFRACTION21B9 - 13
22X-RAY DIFFRACTION22B14 - 23
23X-RAY DIFFRACTION23B24 - 31
24X-RAY DIFFRACTION24B32 - 39
25X-RAY DIFFRACTION25B40 - 45
26X-RAY DIFFRACTION26B46 - 52
27X-RAY DIFFRACTION27B53 - 64
28X-RAY DIFFRACTION28B65 - 72
29X-RAY DIFFRACTION29B73 - 81
30X-RAY DIFFRACTION30B82 - 97
31X-RAY DIFFRACTION31B98 - 104
32X-RAY DIFFRACTION32B105 - 114
33X-RAY DIFFRACTION33B115 - 122
34X-RAY DIFFRACTION34B123 - 128
35X-RAY DIFFRACTION35B137 - 142
36X-RAY DIFFRACTION36B143 - 146
37X-RAY DIFFRACTION37B147 - 152
38X-RAY DIFFRACTION38B153 - 167
39X-RAY DIFFRACTION39B168 - 178
40X-RAY DIFFRACTION40B179 - 185

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