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- PDB-6pk5: Adenylate kinase from Methanococcus igneus - apo form -

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Basic information

Entry
Database: PDB / ID: 6pk5
TitleAdenylate kinase from Methanococcus igneus - apo form
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase
Function / homology
Function and homology information


adenylate kinase / AMP kinase activity / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase AdkA / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanotorris igneus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoon, S. / Kim, J. / Bae, E. / Phillips Jr., G.N.
Funding support Korea, Republic Of, United States, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)PJ013181 Korea, Republic Of
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: To Be Published
Title: Adenylate kinase from Methanococcus igneus - apo form
Authors: Bae, E.
History
DepositionJun 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Adenylate kinase
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,53821
Polymers135,0066
Non-polymers53215
Water2,504139
1
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,75110
Polymers67,5033
Non-polymers2487
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-113 kcal/mol
Surface area27580 Å2
MethodPISA
2
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,78711
Polymers67,5033
Non-polymers2848
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-121 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.710, 68.710, 257.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 22501.016 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanotorris igneus (archaea) / Gene: adkA, adk / Production host: Escherichia coli (E. coli) / References: UniProt: P43408, adenylate kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 30%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. obs: 60464 / % possible obs: 99.8 % / Redundancy: 5.89 % / CC1/2: 0.997 / Net I/σ(I): 9.08
Reflection shellResolution: 2.3→2.44 Å / Mean I/σ(I) obs: 1.04 / Num. unique obs: 9674 / CC1/2: 0.402 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→31.332 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.51
RfactorNum. reflection% reflection
Rfree0.2673 1903 3.15 %
Rwork0.2293 --
obs0.2306 60422 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→31.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8844 0 15 139 8998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158923
X-RAY DIFFRACTIONf_angle_d1.53712006
X-RAY DIFFRACTIONf_dihedral_angle_d12.9885572
X-RAY DIFFRACTIONf_chiral_restr0.0721453
X-RAY DIFFRACTIONf_plane_restr0.0091521
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)
12.6328-0.2678-0.23913.76160.58425.4190.12490.1152-0.4063-0.2731-0.2011-0.20251.11180.15310.05310.83190.08710.03750.40190.0470.5167-61.6687-24.4903-25.7362
23.44910.80360.72773.4166-0.48835.0442-0.15140.5930.4483-0.43550.0545-0.4172-0.58230.67250.0350.5977-0.06910.07340.55680.07930.5443-49.78113.9604-27.1288
33.5745-0.57650.63013.06330.41225.33910.11870.2698-0.0299-0.0536-0.18960.553-0.0495-0.94870.02250.4895-0.00580.00840.5401-0.01330.4612-80.2354-0.0659-26.0979
43.635-0.52520.02533.6127-0.99065.0001-0.08680.0185-0.29180.1749-0.0538-0.33930.52320.65630.07790.4996-0.00280.00290.37870.00990.4854-45.9007-11.674817.8148
52.4242-0.2365-0.25712.76190.71874.13830.0495-0.1834-0.22910.1104-0.13170.4580.4492-0.50570.05460.5579-0.19010.04720.45110.00060.5481-76.3663-17.090618.9367
61.6572-0.4827-0.22662.1620.66794.6742-0.07580.02750.4291-0.034-0.0249-0.1484-0.69540.11780.0750.6035-0.1036-0.03940.32730.03840.5554-66.067611.877417.9962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'

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