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- PDB-5ycb: Crystal structure of notothenia coriiceps adenylate kinase variant -

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Basic information

Entry
Database: PDB / ID: 5ycb
TitleCrystal structure of notothenia coriiceps adenylate kinase variant
Componentsadenylate kinase
KeywordsTRANSFERASE / phosphorylation
Function / homology
Function and homology information


nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process / phosphorylation ...nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase isoenzyme 1
Similarity search - Component
Biological speciesNotothenia coriiceps (black rockcod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.272 Å
AuthorsBae, E. / Kim, J. / Moon, S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01111201 Korea, Republic Of
National Research Foundation of KoreaNRF-2016R1D1A1A09916821 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of notothenia coriiceps adenylate kinase variant
Authors: Bae, E. / Kim, J. / Moon, S.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: adenylate kinase
B: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6806
Polymers42,6552
Non-polymers2,0254
Water1,47782
1
A: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3403
Polymers21,3281
Non-polymers1,0122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-10 kcal/mol
Surface area9580 Å2
MethodPISA
2
B: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3403
Polymers21,3281
Non-polymers1,0122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40 Å2
ΔGint-2 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.284, 105.284, 84.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein adenylate kinase /


Mass: 21327.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Notothenia coriiceps (black rockcod) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R2JFU5*PLUS
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.26M Lithium sulfate, 45% PEG400, 0.1M Acetate pH4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 22461 / % possible obs: 100 % / Redundancy: 23.2 % / Rpim(I) all: 0.021 / Net I/σ(I): 38.63
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 20.5 % / Mean I/σ(I) obs: 6.97 / Num. unique obs: 2192 / Rpim(I) all: 0.146 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X6K
Resolution: 2.272→36.652 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.46
RfactorNum. reflection% reflection
Rfree0.2161 1117 5 %
Rwork0.167 --
obs0.1694 22335 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.272→36.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 124 82 3105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083067
X-RAY DIFFRACTIONf_angle_d1.184141
X-RAY DIFFRACTIONf_dihedral_angle_d14.9531163
X-RAY DIFFRACTIONf_chiral_restr0.041458
X-RAY DIFFRACTIONf_plane_restr0.005508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2722-2.37560.26661350.19592561X-RAY DIFFRACTION99
2.3756-2.50080.26121370.18852611X-RAY DIFFRACTION100
2.5008-2.65740.22721380.18372612X-RAY DIFFRACTION100
2.6574-2.86260.24441370.17512617X-RAY DIFFRACTION100
2.8626-3.15050.25831390.18362639X-RAY DIFFRACTION100
3.1505-3.6060.22191410.17112653X-RAY DIFFRACTION100
3.606-4.54190.19171410.14222693X-RAY DIFFRACTION100
4.5419-36.65660.19131490.16572832X-RAY DIFFRACTION100
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)
13.8792-2.6664-0.7845.7893-1.06773.20290.1754-0.25540.28230.43220.1659-0.3876-0.01640.9743-0.28740.3153-0.09760.08380.5269-0.08250.3221-28.5657-6.063-15.3884
26.64563.85531.5878.45092.57013.18740.26220.07240.2629-0.2302-0.3365-0.6382-0.40950.1663-0.03760.4169-0.06620.09240.33560.03750.3341-27.61071.7935-23.0597
33.6393-2.1761-0.45376.881.47582.06780.59720.4940.6098-0.8609-0.5763-0.5842-0.00810.028-0.03340.36170.02040.07720.37860.04750.3418-20.0023-13.0795-25.4085
49.5767-2.05110.18816.32030.11933.65240.37580.3301-0.6598-0.4585-0.25190.35190.149-0.0750.09120.37370.03740.01280.3543-0.03920.2634-22.5826-24.7416-27.309
56.0237-0.2011-1.00038.09570.39952.76570.325-0.78950.1520.2601-0.5772-0.9376-0.03550.1730.00620.205-0.028-0.00520.4277-0.00160.3017-18.8683-15.2308-15.2538
68.32040.3898-0.33344.9714-0.61463.99340.1966-0.41840.55490.1289-0.1665-0.9587-0.31370.54230.08740.2341-0.01770.04940.3909-0.01640.4214-23.3289-7.0333-15.9895
72.47870.98380.72596.36021.34497.369-0.3492-0.1865-0.97290.14960.2761-0.30190.49891.0470.09270.27150.0790.03660.41150.04780.3847-27.7667-17.0486-8.3515
86.7582-1.5987-0.2484.0749-0.6626.0090.0051-0.68680.1128-0.09930.037-0.1409-0.3946-0.7176-0.04860.1936-0.0337-0.00070.2317-0.00190.3041-34.9485-6.586-15.4323
97.956-2.81343.17117.94390.53815.0260.49031.254-0.4996-1.2634-0.58430.36540.40980.30460.09330.41070.0791-0.03290.4875-0.05240.4167-36.6219-16.0274-32.9591
103.721-0.7143-0.40316.69810.72487.6750.1672-0.6192-0.4208-0.2221-0.24190.5328-0.0062-0.6760.17610.2573-0.01930.06010.36650.0280.3192-38.7585-12.458-11.2318
115.9262-1.64043.30384.49-3.91244.010.02090.31510.1085-0.0108-0.1144-0.0032-0.6729-0.65310.1660.27270.07930.01340.3475-0.05120.3357-41.0329-1.8672-20.4813
127.51161.0012-1.6145.00683.98463.97440.7644-0.00070.8213-0.2863-0.01150.3796-1.5149-0.4057-0.70940.49220.03920.1270.34310.05430.431-35.88375.5051-20.507
135.0204-0.6603-0.41787.74131.79232.89310.0005-0.48610.0490.16760.239-0.7515-0.31610.0126-0.13450.2908-0.0475-0.04760.41060.09010.3109-49.7903-22.69542.0337
142.9141-0.17531.19460.92830.2851.05220.1596-0.5025-0.20950.2292-0.13730.0414-0.02580.0266-0.05110.307-0.09-0.01320.47460.12010.3255-57.9043-26.02295.9735
154.334-3.3556-4.368.10233.96784.44550.38551.126-0.1052-0.6738-0.50960.5524-0.3045-0.40990.1090.3353-0.0019-0.07520.49830.04840.3332-70.1812-22.4915-9.0617
166.08092.04331.51256.64614.83325.47710.1206-0.14560.695-0.3769-0.23260.5442-0.6039-0.56240.23990.2850.0191-0.00170.41320.09710.4079-61.731-15.0044-1.6618
177.89560.1001-1.49246.03170.42616.95350.2121-0.28510.4433-0.1167-0.16380.2676-0.3024-0.3919-0.11620.1655-0.0148-0.00960.33170.04820.3566-54.1787-14.65372.1268
184.9235-0.85911.00597.00893.72524.0570.44450.15010.0939-0.5373-0.388-1.0051-0.0780.0465-0.21850.23850.02230.03080.31020.11270.2812-45.5718-21.05990.572
192.82480.5384-0.11469.26571.98077.74380.050.6955-1.7391-0.51440.01620.71570.8828-0.4369-0.00990.47630.0398-0.09790.4483-0.01760.7761-53.7623-40.022-6.5613
204.60834.43560.50689.8927-0.90853.6388-0.27971.0063-0.5274-0.73420.40490.10090.0243-0.3968-0.04260.37290.0661-0.01480.526-0.02130.3501-56.1016-30.7013-13.0457
212.05481.2497-1.13667.0415-0.63141.08060.216-0.1278-0.21350.0512-0.0921-0.67240.0385-0.0876-0.02250.2186-0.033-0.02530.35610.1030.4102-42.0077-22.6334-2.5785
224.66-1.1457-0.79358.87520.59155.98-0.0733-0.8172-0.40980.6852-0.3062-0.2727-0.26450.41890.09150.332-0.0677-0.11430.5450.22060.4798-42.0192-29.74799.6042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 98 )
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 108 )
8X-RAY DIFFRACTION8chain 'A' and (resid 109 through 121 )
9X-RAY DIFFRACTION9chain 'A' and (resid 122 through 156 )
10X-RAY DIFFRACTION10chain 'A' and (resid 157 through 167 )
11X-RAY DIFFRACTION11chain 'A' and (resid 168 through 178 )
12X-RAY DIFFRACTION12chain 'A' and (resid 179 through 193 )
13X-RAY DIFFRACTION13chain 'B' and (resid 8 through 20 )
14X-RAY DIFFRACTION14chain 'B' and (resid 21 through 49 )
15X-RAY DIFFRACTION15chain 'B' and (resid 50 through 63 )
16X-RAY DIFFRACTION16chain 'B' and (resid 64 through 82 )
17X-RAY DIFFRACTION17chain 'B' and (resid 83 through 108 )
18X-RAY DIFFRACTION18chain 'B' and (resid 109 through 121 )
19X-RAY DIFFRACTION19chain 'B' and (resid 122 through 136 )
20X-RAY DIFFRACTION20chain 'B' and (resid 137 through 156 )
21X-RAY DIFFRACTION21chain 'B' and (resid 157 through 178 )
22X-RAY DIFFRACTION22chain 'B' and (resid 179 through 193 )

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