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- PDB-4jla: Crystal Structure of Adenylate kinase with 2 ADP's in the active site -

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Basic information

Entry
Database: PDB / ID: 4jla
TitleCrystal Structure of Adenylate kinase with 2 ADP's in the active site
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ADP binding / phosphoryl transfer reaction
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity ...nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / intracellular membrane-bounded organelle / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase, active site lid domain superfamily / Adenylate kinase subfamily / 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
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsCho, Y.-J. / Kern, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The energy landscape of adenylate kinase during catalysis.
Authors: Kerns, S.J. / Agafonov, R.V. / Cho, Y.J. / Pontiggia, F. / Otten, R. / Pachov, D.V. / Kutter, S. / Phung, L.A. / Murphy, P.N. / Thai, V. / Alber, T. / Hagan, M.F. / Kern, D.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Feb 28, 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: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6746
Polymers45,9662
Non-polymers1,7094
Water4,089227
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8373
Polymers22,9831
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8373
Polymers22,9831
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.940, 73.890, 87.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenylate kinase / AK / ATP-AMP transphosphorylase


Mass: 22982.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: adk, aq_078 / Production host: Escherichia coli (E. coli) / References: UniProt: O66490, adenylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 47.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M Sodium Acetate trihydrate, 0.2M Ammonium Acetate, 30% w/v Polyethylene Glycol 4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→43.9 Å / Num. all: 150661 / Num. obs: 23143 / % possible obs: 91.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 31.37 Å2 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
2.12-2.231.8199.9
6.7-43.918199.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_860refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→43.9 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8041 / SU ML: 0.62 / σ(F): 1.33 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 1167 5.09 %
Rwork0.1857 --
obs0.1892 22909 90.39 %
all-24076 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.497 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 110.03 Å2 / Biso mean: 38.9068 Å2 / Biso min: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1--9.6933 Å20 Å2-0 Å2
2--13.9019 Å2-0 Å2
3----4.2086 Å2
Refinement stepCycle: LAST / Resolution: 2.12→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 108 227 3571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083436
X-RAY DIFFRACTIONf_angle_d1.2344657
X-RAY DIFFRACTIONf_chiral_restr0.067514
X-RAY DIFFRACTIONf_plane_restr0.006585
X-RAY DIFFRACTIONf_dihedral_angle_d17.0881371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.12-2.21650.2861840.208629133097100
2.2165-2.33340.45071050.2882000210568
2.3334-2.47950.2961670.211529563123100
2.4795-2.6710.33211330.228727052838100
2.671-2.93970.33171590.200127252884100
2.9397-3.3650.26471500.19630093159100
3.365-4.23890.22621150.16352240235574
4.2389-43.90940.1841540.154931943348100
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)
11.9839-0.3524-0.11622.05780.12942.9804-0.01090.0473-0.1844-0.1327-0.04760.14250.1364-0.33270.03210.1187-0.00710.0150.1620.00390.176413.9493-8.8921-7.2495
23.2252-0.8466-0.80273.1119-1.39023.4652-0.3451-0.6856-0.43930.34960.1614-0.2588-0.08760.42660.08820.137-0.0030.04810.29970.07550.208532.6451-3.1262-1.7644
33.19810.1412-0.42643.2178-0.60342.5059-0.11020.49890.2916-0.32830.036-0.143-0.38850.0030.03150.1847-0.03060.0090.15660.03150.181120.89810.1364-12.9242
42.99710.2220.31361.8564-0.28695.54440.0426-0.06010.22920.0567-0.10830.0229-0.39730.04490.06210.1150.045-0.01540.13340.02060.147512.22640.4186-6.652
52.9579-0.11221.07374.36350.69712.68940.2202-0.326-0.56470.3813-0.031-0.2980.43270.0729-0.16580.19980.0408-0.02910.29740.06630.271420.3705-14.21288.3553
62.90810.41970.10472.2441-0.4842.49460.0379-0.13410.54410.35060.05580.2727-0.4312-0.3392-0.03030.19990.05520.02230.1485-0.00970.212310.80554.4511-1.2299
73.37920.5898-1.40594.2013-3.29824.1358-0.148-0.018-0.1062-0.23240.34030.20550.1306-1.3084-0.2340.1684-0.017-0.03050.28080.01610.31462.0263-10.4255-5.1873
81.32681.6615-0.39542.5982-1.87753.80730.01960.16070.0978-0.20820.08320.2584-0.001-0.40790.07710.1870.00720.03620.2922-0.13940.208813.0351-30.6933-23.643
92.3198-0.43631.02752.7684-0.28513.3872-0.18930.4204-0.6095-0.28970.13760.5927-0.168-0.59030.13450.1774-0.07870.01550.4159-0.12970.277414.6119-37.3897-29.6197
102.05290.05540.04583.7231.08925.1938-0.1093-0.0287-0.25510.0139-0.2313-0.1387-0.0770.04710.27780.11380.0070.08280.29810.00080.211129.9761-39.0849-25.5765
114.43820.4277-1.47982.85560.30081.8710.0870.6651-0.0072-0.4902-0.07030.171-0.131-0.20840.06650.12670.0350.01210.1706-0.11360.111522.3082-27.7404-29.1064
121.4292-0.66940.51793.65610.41082.0630.03960.06990.0460.1636-0.12410.3705-0.301-0.16680.08940.1615-0.0024-0.00550.2405-0.10440.149416.6034-28.4595-21.9304
134.6554-1.3289-0.24284.24574.95546.18760.53741.1105-0.6535-0.7631-0.264-0.03290.46620.09440.25931.0666-0.01490.23490.4845-0.14990.473812.3037-49.0075-24.352
143.7077-1.64381.43513.90631.86352.52320.0894-0.0598-1.1771-0.5374-0.09780.33320.6691-0.3720.02530.6523-0.19950.07710.3056-0.04730.47619.0263-48.4214-16.0001
151.9549-1.07560.21056.5762-2.48213.5315-0.0443-0.25390.04360.543-0.2507-0.3434-0.18940.27340.24710.2124-0.07310.05870.3103-0.06980.16622.1924-28.3076-14.3105
165.72162.95291.1052.47131.074.44690.11350.02890.2270.1489-0.42240.7818-0.0758-1.24930.1340.22630.03080.03160.4329-0.17910.46314.1183-26.1989-21.2536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:34)A1 - 34
2X-RAY DIFFRACTION2(chain A and resid 35:63)A35 - 63
3X-RAY DIFFRACTION3(chain A and resid 64:94)A64 - 94
4X-RAY DIFFRACTION4(chain A and resid 95:119)A95 - 119
5X-RAY DIFFRACTION5(chain A and resid 120:160)A120 - 160
6X-RAY DIFFRACTION6(chain A and resid 161:190)A161 - 190
7X-RAY DIFFRACTION7(chain A and resid 191:203)A191 - 203
8X-RAY DIFFRACTION8(chain B and resid 1:18)B1 - 18
9X-RAY DIFFRACTION9(chain B and resid 19:37)B19 - 37
10X-RAY DIFFRACTION10(chain B and resid 38:73)B38 - 73
11X-RAY DIFFRACTION11(chain B and resid 74:92)B74 - 92
12X-RAY DIFFRACTION12(chain B and resid 93:125)B93 - 125
13X-RAY DIFFRACTION13(chain B and resid 126:133)B126 - 133
14X-RAY DIFFRACTION14(chain B and resid 134:151)B134 - 151
15X-RAY DIFFRACTION15(chain B and resid 152:181)B152 - 181
16X-RAY DIFFRACTION16(chain B and resid 182:203)B182 - 203

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