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- PDB-6psp: Adenylate kinase from Methanococcus igneus - AP5A bound form -

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Basic information

Entry
Database: PDB / ID: 6psp
TitleAdenylate kinase from Methanococcus igneus - AP5A bound form
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase
Function / homology
Function and homology information


adenylate kinase / adenylate kinase activity / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase AdkA / AAA domain / 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
Similarity search - Component
Biological speciesMethanotorris igneus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 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 - AMP bound form
Authors: Bae, E.
History
DepositionJul 13, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)140,50412
Polymers135,0066
Non-polymers5,4986
Water77543
1
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2526
Polymers67,5033
Non-polymers2,7493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-48 kcal/mol
Surface area23640 Å2
MethodPISA
2
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2526
Polymers67,5033
Non-polymers2,7493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-48 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.443, 122.627, 83.721
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 2 - 192 / Label seq-ID: 2 - 192

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF

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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-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C20H29N10O22P5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 4mM AP5A 17% (w/v) polyethylene 33500, 250 mM sodium malonate

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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: 0.997933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997933 Å / Relative weight: 1
ReflectionResolution: 2.25→33.189 Å / Num. obs: 227650 / % possible obs: 93.4 % / Redundancy: 3.85 % / CC1/2: 0.999 / Net I/σ(I): 10.82
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 2.75 % / Num. unique obs: 7203 / CC1/2: 0.282 / % possible all: 70.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.252→33.189 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1976 3.88 %
Rwork0.2151 48912 -
obs0.2167 50888 80.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.45 Å2 / Biso mean: 71.0591 Å2 / Biso min: 37.68 Å2
Refinement stepCycle: final / Resolution: 2.252→33.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8922 0 486 43 9451
Biso mean--71.06 58.61 -
Num. residues----1146
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5916X-RAY DIFFRACTION7.843TORSIONAL
12B5916X-RAY DIFFRACTION7.843TORSIONAL
13C5916X-RAY DIFFRACTION7.843TORSIONAL
14D5916X-RAY DIFFRACTION7.843TORSIONAL
15E5916X-RAY DIFFRACTION7.843TORSIONAL
16F5916X-RAY DIFFRACTION7.843TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2523-2.30860.4048990.3687141734
2.3086-2.3711100000000.3443195043
2.3711-2.44080.3345990.339217851
2.4408-2.51960.3624990.3331266261
2.5196-2.60960.35871980.3077315174
2.6096-2.7140.3295980.287356881
2.714-2.83750.3271970.2846375788
2.8375-2.9870.3638990.2913428597
2.987-3.1740.36261980.26854283100
3.174-3.41880.27181980.2564328100
3.4188-3.76240.26881960.23574333100
3.7624-4.30590.2237990.18864394100
4.3059-5.42110.23751980.17974341100
5.4211-33.1890.20171980.1667426597
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)
13.3424-0.0168-0.07033.374-0.4642.89-0.1354-0.11270.129-0.10180.009-1.2992-0.20071.5888-0.06890.3257-0.01210.03081.02610.02420.876721.9545-3.712838.8313
22.20840.0178-0.56914.6094-0.42974.6750.07330.29840.3067-0.31450.02970.6566-0.3945-0.49-0.02430.31380.0699-0.06290.38720.03110.4617-7.37846.721733.6315
33.92041.8228-1.02755.6896-0.49285.7875-0.36250.3634-0.8776-1.03110.1828-0.45131.45670.3179-0.10610.80.07630.1020.3309-0.06940.5572-0.7787-23.940430.5562
42.9192-0.6769-0.08972.70060.49562.8921-0.2382-0.6027-0.62180.76260.0703-0.41250.93380.87940.09720.81720.1723-0.0210.91060.20330.61856.7465-26.41474.4933
53.7831.0904-0.56723.9321-0.12184.3998-0.0801-0.3919-0.00970.29690.17141.1110.1638-0.9621-0.0380.52420.00180.11030.75850.14070.7128-22.2115-14.739869.5861
62.88960.4515-1.44155.0693-0.78764.84240.3048-0.84750.51131.3165-0.1439-0.5082-0.86310.7978-0.13641.0408-0.2135-0.01720.8454-0.09350.57171.33134.525877.4644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A2 - 192
2X-RAY DIFFRACTION2chain 'B'B2 - 192
3X-RAY DIFFRACTION3chain 'C'C2 - 192
4X-RAY DIFFRACTION4chain 'D'D2 - 192
5X-RAY DIFFRACTION5chain 'E'E2 - 192
6X-RAY DIFFRACTION6chain 'F'F2 - 192

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