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- PDB-5ycd: Crystal structure of Poecilia reticulata adenylate kinase -

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Basic information

Entry
Database: PDB / ID: 5ycd
TitleCrystal structure of Poecilia reticulata adenylate kinase
ComponentsAdenylayte kinase
KeywordsTRANSFERASE / phosphorylation
Function / homology
Function and homology information


nucleoside triphosphate adenylate kinase activity / (d)CMP 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 ...nucleoside triphosphate adenylate kinase activity / (d)CMP 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 / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase isoenzyme 1
Similarity search - Component
Biological speciesPoecilia reticulata (guppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 Poecilia reticulata adenylate kinase
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: Adenylayte kinase
B: Adenylayte kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2446
Polymers42,3632
Non-polymers1,8814
Water5,567309
1
A: Adenylayte kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1223
Polymers21,1821
Non-polymers9412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6 kcal/mol
Surface area9150 Å2
MethodPISA
2
B: Adenylayte kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1223
Polymers21,1821
Non-polymers9412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-4 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.790, 81.505, 120.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenylayte kinase


Mass: 21181.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poecilia reticulata (guppy) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSM2*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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 27.5% PEG3350, 0.1M Citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979933 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: 0.979933 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 37999 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rpim(I) all: 0.027 / Net I/σ(I): 28.01
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 5.13 / Num. unique obs: 3759 / Rpim(I) all: 0.193 / % 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: 1.8→31.178 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.33
RfactorNum. reflection% reflection
Rfree0.2091 1896 5 %
Rwork0.1665 --
obs0.1686 37930 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→31.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 116 309 3378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073111
X-RAY DIFFRACTIONf_angle_d1.1934195
X-RAY DIFFRACTIONf_dihedral_angle_d12.8411177
X-RAY DIFFRACTIONf_chiral_restr0.041468
X-RAY DIFFRACTIONf_plane_restr0.004516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7998-1.84480.2551300.20232475X-RAY DIFFRACTION97
1.8448-1.89470.26681330.19912533X-RAY DIFFRACTION100
1.8947-1.95050.25461340.2012550X-RAY DIFFRACTION100
1.9505-2.01340.19741340.18242526X-RAY DIFFRACTION100
2.0134-2.08530.21861340.18222544X-RAY DIFFRACTION100
2.0853-2.16880.22891340.17862564X-RAY DIFFRACTION100
2.1688-2.26750.21291340.17072562X-RAY DIFFRACTION100
2.2675-2.3870.21551340.17082542X-RAY DIFFRACTION100
2.387-2.53650.23281350.18282570X-RAY DIFFRACTION100
2.5365-2.73220.24221370.17922580X-RAY DIFFRACTION100
2.7322-3.0070.23251350.18152569X-RAY DIFFRACTION100
3.007-3.44160.21111380.16222617X-RAY DIFFRACTION100
3.4416-4.33420.16991380.13952637X-RAY DIFFRACTION100
4.3342-31.18220.18391460.15142765X-RAY DIFFRACTION100
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)
15.4022-1.99620.03844.8074-1.07292.38760.01770.0374-0.5917-0.19160.2774-0.44090.78580.2204-0.03550.35260.0719-0.06620.1861-0.0760.2293-7.5275-8.7438-20.7009
26.73791.5727-0.9841.7585-0.38321.99790.2513-0.4469-0.13070.2109-0.1486-0.040.20330.0866-0.12280.2190.0148-0.02770.1846-0.01790.1067-7.5419-2.6704-11.7914
34.8471-4.53954.22764.7011-3.69494.76470.0924-0.05481.09460.0530.0325-0.2939-0.44770.85710.09130.1496-0.03150.01320.3169-0.08910.30966.814711.1847-16.3288
42.0618-1.77720.25798.0662-3.10173.8246-0.0381-0.16540.0092-0.20530.0276-0.95030.51530.61190.09310.20730.1167-0.03840.3185-0.0590.24473.1064-2.1371-20.6129
54.3638-1.74061.49333.6402-5.44558.53430.1657-0.1568-0.2195-0.50160.08220.24910.83250.1534-0.14650.28480.0396-0.05830.1542-0.04530.1423-4.8891-7.4474-18.3275
64.1825-0.8079-0.68115.09810.74134.56160.00910.2935-0.222-0.17770.0081-0.23480.44460.18630.00950.21020.0268-0.05180.1623-0.02890.0672-7.8338-4.9178-26.975
75.74885.55983.09018.4584.30422.77130.08390.16980.070.22690.0278-0.0318-0.29720.2395-0.14730.19780.04890.03070.20610.01970.156-13.257214.474-13.0192
86.14091.32671.80347.74834.47372.794-0.16080.29810.8411-0.80060.077-0.3056-0.7314-0.01830.02690.30840.04550.01150.23130.08360.2735-10.115614.2207-24.5698
91.8944-0.0058-0.83141.0870.6713.52410.11120.17010.0911-0.2334-0.1170.23710.0342-0.44320.03010.201-0.0018-0.050.2729-0.03240.1376-17.0856-2.1923-26.8735
103.8071-5.1356-2.06447.62971.364.30210.1068-0.1798-0.34120.02620.06910.45220.7205-0.6648-0.17160.2659-0.0996-0.03450.32360.02810.2002-22.2117-8.1689-15.2287
116.29614.9440.81036.21070.17892.4989-0.050.0281-0.0169-0.22660.0785-0.2127-0.4660.0822-0.01310.2436-0.03740.00540.18720.01780.1402-0.78038.31088.383
123.8935-0.84860.35662.48860.28792.03110.20290.2521-0.5432-0.1-0.0855-0.12410.11990.1919-0.11750.1454-0.0116-0.03160.1567-0.04180.1863.0123-3.89612.0422
134.34971.18510.04477.6565-2.25954.60410.06270.0132-0.2495-0.0224-0.0298-0.4031-0.20490.2796-0.00860.1276-0.0413-0.00240.1552-0.04790.13175.28712.77668.0029
141.75360.30440.75064.18491.61522.79350.1315-0.0344-0.29770.0469-0.07780.01610.17970.01-0.050.1496-0.0224-0.00470.17780.06860.1215-4.7325-5.39119.0598
155.1832-3.2767-3.90537.65572.12318.2381-0.0928-0.1875-0.71190.5823-0.09470.00681.1426-0.22170.23090.3597-0.1329-0.05570.26440.14930.3224-4.535-15.169213.9778
163.6046-0.3732.06041.71260.27525.18090.1332-0.1114-0.32970.1442-0.11940.389-0.1481-0.5903-0.01490.13770.01660.0210.2384-0.00880.2029-13.54433.462210.5267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 63 )
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 83 )
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 98 )
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 121 )
7X-RAY DIFFRACTION7chain 'A' and (resid 122 through 142 )
8X-RAY DIFFRACTION8chain 'A' and (resid 143 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 1 through 20 )
12X-RAY DIFFRACTION12chain 'B' and (resid 21 through 63 )
13X-RAY DIFFRACTION13chain 'B' and (resid 64 through 98 )
14X-RAY DIFFRACTION14chain 'B' and (resid 99 through 142 )
15X-RAY DIFFRACTION15chain 'B' and (resid 143 through 156 )
16X-RAY DIFFRACTION16chain 'B' and (resid 157 through 193 )

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