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- PDB-5ycf: Crystal structure of Xiphophorus maculatus adenylate kinase -

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Basic information

Entry
Database: PDB / ID: 5ycf
TitleCrystal structure of Xiphophorus maculatus adenylate kinase
ComponentsAdenylate kinase isoenzyme 1
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 / AMP 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 / adenylate kinase / AMP 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 speciesXiphophorus maculatus (southern platyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.938 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 Xiphophorus maculatus 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
B: Adenylate kinase isoenzyme 1
A: Adenylate kinase isoenzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2244
Polymers42,3912
Non-polymers1,8332
Water5,927329
1
B: Adenylate kinase isoenzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1122
Polymers21,1961
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-3 kcal/mol
Surface area9240 Å2
MethodPISA
2
A: Adenylate kinase isoenzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1122
Polymers21,1961
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.033, 79.779, 122.386
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 Adenylate kinase isoenzyme 1 / AK 1 / ATP-AMP transphosphorylase 1 / ATP:AMP phosphotransferase / Adenylate monophosphate kinase / Myokinase


Mass: 21195.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xiphophorus maculatus (southern platyfish)
Gene: AK1 / Production host: Escherichia coli (E. coli)
References: UniProt: M4AA20, adenylate kinase, nucleoside-diphosphate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 47.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Citric acid, pH 3.5, 27.5% PEG3350

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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: 1.95→50 Å / Num. obs: 30295 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rpim(I) all: 0.055 / Net I/σ(I): 12.81
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.52 / Num. unique obs: 2943 / Rpim(I) all: 0.252 / % possible all: 98.9

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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: 1.938→39.889 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 1487 5.03 %
Rwork0.1841 --
obs0.1872 29539 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.938→39.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 114 329 3351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073065
X-RAY DIFFRACTIONf_angle_d1.1194134
X-RAY DIFFRACTIONf_dihedral_angle_d13.7391158
X-RAY DIFFRACTIONf_chiral_restr0.041464
X-RAY DIFFRACTIONf_plane_restr0.004506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9377-2.00030.3102910.23871962X-RAY DIFFRACTION76
2.0003-2.07180.29841300.22182414X-RAY DIFFRACTION92
2.0718-2.15470.27131390.2172535X-RAY DIFFRACTION97
2.1547-2.25280.27561350.20312562X-RAY DIFFRACTION99
2.2528-2.37150.27531460.19872562X-RAY DIFFRACTION99
2.3715-2.52010.26041220.20232616X-RAY DIFFRACTION99
2.5201-2.71460.26351500.20492623X-RAY DIFFRACTION99
2.7146-2.98770.27171350.20012632X-RAY DIFFRACTION99
2.9877-3.41990.26211490.17942657X-RAY DIFFRACTION100
3.4199-4.30790.20441490.14822663X-RAY DIFFRACTION100
4.3079-39.89790.19531410.15712826X-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)
12.11491.1931-0.61081.9882-0.42281.89680.09140.16390.28850.08810.00610.24950.1522-0.0125-0.10620.10350.00990.00290.10750.00920.097845.2765-6.1488126.618
21.113-0.61310.08752.2764-0.39281.34710.09660.18790.5017-0.01440.07070.0988-0.0318-0.1365-0.10330.11-0.00360.02790.12310.05080.336934.1772.6392128.3722
32.2320.9258-0.20453.7146-0.41992.21140.1243-0.33950.36480.23050.03180.22950.02490.0424-0.14670.1584-0.01910.0340.1142-0.05270.13843.3966-3.4441137.4157
41.38870.3508-0.52181.17240.34882.39480.1682-0.11040.6008-0.00090.04650.1112-0.18410.2732-0.12380.115-0.01230.01590.1474-0.06940.289751.4236.0997131.8266
52.1683-0.84550.30982.55471.34331.78330.1953-0.05740.5591-0.41120.06110.3098-0.44-0.072-0.18810.30310.02640.11090.12560.05490.300949.70676.6344100.1362
61.3595-0.65180.75231.9971.22961.91670.2828-0.7370.75230.0056-0.11830.018-0.4174-0.07790.17010.2328-0.0630.0910.2638-0.14740.264554.81366.3462110.2145
71.9846-1.10430.5321.09520.36542.09660.4299-0.8520.27260.218-0.22510.1074-0.2745-0.2604-0.08020.1551-0.04260.03590.3077-0.02610.127840.3431-1.7063108.4852
84.631-4.0472-6.24227.0845.06929.15840.04930.136-0.46180.37850.0801-0.02180.4201-0.5716-0.11140.1869-0.0542-0.07140.21760.09130.264234.1279-11.6746104.5744
93.6562-2.95330.25218.49691.25262.86730.0585-0.15110.2526-0.28110.38490.8449-0.3201-0.279-0.05930.16330.04810.08210.25160.06050.264237.411.101599.8369
103.3717-0.91410.85857.2813.47132.17070.1243-0.40840.63040.17720.21050.1804-0.29980.1131-0.10160.3122-0.02590.16080.2083-0.04850.238945.08867.3978103.1519
111.5760.4816-0.88353.43410.28012.43550.19620.3160.5061-0.3672-0.11750.2814-0.2572-0.1211-0.11180.23990.04120.07740.17350.04650.116248.56954.362794.1578
121.18421.1417-0.46234.5216-1.99566.3022-0.02470.2403-0.2143-0.1510.0440.10720.4083-0.5046-0.01050.1215-0.0155-0.02210.1669-0.02840.099353.996-14.2123108.8812
138.45331.6232-1.77093.803-2.0842.9357-0.13480.417-1.0377-0.6301-0.1111-0.06831.02810.09470.04390.3360.0635-0.0010.2203-0.07920.173950.6261-14.631797.091
141.5767-0.32011.5290.9229-0.78553.30620.18720.14250.1737-0.1742-0.1074-0.0892-0.17810.4293-0.05410.186-0.00430.05690.22230.03690.128957.81031.582894.3477
155.2244-1.5812.25215.4978-2.64744.86380.0568-0.31620.92320.2004-0.2544-0.3468-0.4980.45650.07480.1965-0.16050.07850.3511-0.17230.318663.05837.6691105.8732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 34 )
2X-RAY DIFFRACTION2chain 'B' and (resid 35 through 98 )
3X-RAY DIFFRACTION3chain 'B' and (resid 99 through 121 )
4X-RAY DIFFRACTION4chain 'B' and (resid 122 through 193 )
5X-RAY DIFFRACTION5chain 'A' and (resid 5 through 20 )
6X-RAY DIFFRACTION6chain 'A' and (resid 21 through 34 )
7X-RAY DIFFRACTION7chain 'A' and (resid 35 through 49 )
8X-RAY DIFFRACTION8chain 'A' and (resid 50 through 63 )
9X-RAY DIFFRACTION9chain 'A' and (resid 64 through 82 )
10X-RAY DIFFRACTION10chain 'A' and (resid 83 through 98 )
11X-RAY DIFFRACTION11chain 'A' and (resid 99 through 121 )
12X-RAY DIFFRACTION12chain 'A' and (resid 122 through 142 )
13X-RAY DIFFRACTION13chain 'A' and (resid 143 through 156 )
14X-RAY DIFFRACTION14chain 'A' and (resid 157 through 178 )
15X-RAY DIFFRACTION15chain 'A' and (resid 179 through 193 )

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