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- PDB-5ycc: Crystal structure of Notothenia coriiceps adenylate kinase variant -

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Basic information

Entry
Database: PDB / ID: 5ycc
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 / (d)CMP kinase activity / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process ...nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / (d)CMP kinase activity / 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: 2.7 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)44,6526
Polymers42,6272
Non-polymers2,0254
Water50428
1
A: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4224
Polymers21,3141
Non-polymers1,1083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area9140 Å2
MethodPISA
2
B: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2302
Polymers21,3141
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-6 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.200, 105.200, 83.779
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: 21313.662 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


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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.14M 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: 2.7→50 Å / Num. obs: 13506 / % possible obs: 99.9 % / Redundancy: 16 % / Rpim(I) all: 0.036 / Net I/σ(I): 22.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1313 / Rpim(I) all: 0.204 / % 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

5x6k


Resolution: 2.7→32.347 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.27
RfactorNum. reflection% reflection
Rfree0.2225 695 5.18 %
Rwork0.1679 --
obs0.1709 13426 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→32.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 124 28 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083040
X-RAY DIFFRACTIONf_angle_d1.164106
X-RAY DIFFRACTIONf_dihedral_angle_d14.8891150
X-RAY DIFFRACTIONf_chiral_restr0.04454
X-RAY DIFFRACTIONf_plane_restr0.005504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6946-2.90250.31341170.21212481X-RAY DIFFRACTION99
2.9025-3.19430.24861450.18912494X-RAY DIFFRACTION100
3.1943-3.6560.24161330.15992534X-RAY DIFFRACTION100
3.656-4.60410.1851520.14182546X-RAY DIFFRACTION100
4.6041-32.34970.21551480.1772676X-RAY DIFFRACTION99
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)
17.2361-0.47931.90356.8028-1.08094.68150.3215-0.18530.4950.25490.07670.14460.2184-0.163-0.16320.1888-0.0890.05740.3738-0.06130.1909-31.2303-6.43-18.2351
28.90962.51950.92762.68981.93633.78310.23850.3180.2082-0.2015-0.6646-0.7237-0.60840.16640.20610.3954-0.02450.14510.2568-0.01140.4692-27.57851.896-23.063
34.8416-0.37971.13729.65491.22595.94880.59870.69881.1021-0.5542-0.4869-0.4867-0.0998-0.1576-0.00910.2524-0.0140.0830.32050.04390.3122-20.4042-12.6107-25.123
44.53180.8082-1.23374.4373-0.78745.33280.35990.2879-0.3858-0.4468-0.10380.03620.2768-0.177-0.22720.38460.040.04450.4143-0.03130.2026-22.1206-24.4555-27.2232
58.25642.0281-0.99729.05820.79784.63780.1596-0.30670.3626-0.32410.0102-1.084-0.33280.4598-0.1590.1756-0.0171-0.00450.4345-0.02070.328-17.7976-12.8966-15.1129
67.7676-0.9183-0.80545.0820.55035.52730.011-0.07550.26520.43790.3273-0.07850.08990.2987-0.23270.21310.02260.04810.3415-0.01490.2411-26.5437-11.8286-12.7823
74.9935-0.99311.58964.70461.54976.32940.0076-0.92690.2659-0.44710.00050.0183-0.2448-0.9759-0.0490.1698-0.04310.01890.2327-0.00950.3124-34.8979-6.416-15.4219
85.309-2.04320.34947.74270.78295.72760.38830.8489-0.5989-1.1814-0.5520.4007-0.02180.78290.24250.34680.117-0.08330.5016-0.01370.4166-36.5619-16.0283-32.8241
92.8887-1.42440.89116.2406-4.15235.41390.234-0.1206-0.0073-0.1971-0.21850.5077-0.0242-0.2049-0.10290.18620.02950.02050.3255-0.07190.2465-39.8078-7.2839-15.5412
102.95960.5711-1.03898.09633.52585.36650.25410.0680.99420.0317-0.3606-0.4234-1.9029-0.0403-0.06940.39990.0480.13830.30150.01370.4851-35.95035.5832-20.4967
112.4532-0.0971-0.78251.5855-1.63083.61370.19-0.7402-0.49210.22420.0205-0.3849-0.2078-0.0095-0.17590.2959-0.0891-0.07340.51340.16840.4088-50.5574-25.98956.8826
124.89322.36662.80772.38951.7414.06420.3249-0.77870.65470.1246-0.25010.25060.4232-0.0215-0.14880.2111-0.05410.00630.36380.05550.3111-64.472-23.4911.545
138.63711.1878-5.34185.4991-0.17565.8204-0.36770.99980.4039-0.63020.18910.5621-0.10040.08250.1990.316-0.0645-0.10360.45990.15410.3648-67.9034-22.1014-9.7187
146.82910.5614-1.19716.16634.28123.47510.1408-0.66380.65740.0169-0.16960.3957-0.6677-0.98530.02060.267-0.0079-0.03190.4126-0.01240.3905-62.0006-13.19381.5223
155.121-0.1669-1.27097.5601-0.59038.85420.325-0.99950.11540.69370.09960.71190.02420.3803-0.34970.2504-0.10820.03330.54820.14520.3912-55.369-18.10385.987
162.38470.6134-3.4259.06815.40819.3294-0.05550.47680.9761-0.3015-0.281.242-0.8621-0.38810.21690.36080.02660.03210.33290.12310.4639-52.6596-9.4215-3.7739
175.3861-0.3359-0.12677.43782.94764.0820.25220.2128-1.0336-0.5811-0.1989-0.42070.3008-0.0795-0.10.24350.0635-0.06930.31230.08510.2843-49.5562-31.0508-3.4734
187.57584.61610.58826.49340.62541.4147-0.05180.7247-0.4182-0.25190.0249-0.0970.1554-0.13750.0250.32110.02150.01220.47320.01610.2579-51.6927-26.0965-10.1919
190.15650.3962-0.36122.4002-1.02140.91010.0722-0.4836-0.402-0.2671-0.2328-1.21240.45510.5463-0.00090.3683-0.0079-0.09070.41810.15090.5518-40.5269-28.75290.8941
205.89330.460.19883.19883.47549.1876-0.3292-0.9337-0.67310.34040.1714-0.235-0.48680.05530.05090.3422-0.0755-0.17260.56820.24850.5777-41.9523-29.57359.6948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 48 )
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 85 )
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 108 )
7X-RAY DIFFRACTION7chain 'A' and (resid 109 through 121 )
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 156 )
9X-RAY DIFFRACTION9chain 'A' and (resid 157 through 178 )
10X-RAY DIFFRACTION10chain 'A' and (resid 179 through 193 )
11X-RAY DIFFRACTION11chain 'B' and (resid 8 through 34 )
12X-RAY DIFFRACTION12chain 'B' and (resid 35 through 49 )
13X-RAY DIFFRACTION13chain 'B' and (resid 50 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 82 )
15X-RAY DIFFRACTION15chain 'B' and (resid 83 through 98 )
16X-RAY DIFFRACTION16chain 'B' and (resid 99 through 108 )
17X-RAY DIFFRACTION17chain 'B' and (resid 109 through 135 )
18X-RAY DIFFRACTION18chain 'B' and (resid 136 through 167 )
19X-RAY DIFFRACTION19chain 'B' and (resid 168 through 178 )
20X-RAY DIFFRACTION20chain 'B' and (resid 179 through 193 )

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