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- PDB-6hf7: Crystal structure of the adenylate kinase from Methanothermococcu... -

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Basic information

Entry
Database: PDB / ID: 6hf7
TitleCrystal structure of the adenylate kinase from Methanothermococcus thermolithotrophicus co-crystallized with Tb-Xo4
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Protein crystallization / de novo phasing / nucleation / Crystallophore / Tb-Xo4 / molecular glue / Lanthanide complex
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
Tb-Xo4 / TERBIUM(III) ION / Adenylate kinase
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsEngilberge, S. / Wagner, T. / Santoni, G. / Breyton, C. / Shima, S. / Franzetti, B. / Riobe, F. / Maury, O. / Girard, E.
Funding support France, Germany, 2items
OrganizationGrant numberCountry
French National Research AgencyLn23 ANR-13-BS07-0007-01 France
Max Planck Society Germany
CitationJournal: J.Appl.Crystallogr. / Year: 2019
Title: Protein crystal structure determination with the crystallophore, a nucleating and phasing agent.
Authors: Engilberge, S. / Wagner, T. / Santoni, G. / Breyton, C. / Shima, S. / Franzetti, B. / Riobe, F. / Maury, O. / Girard, E.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,12411
Polymers64,4603
Non-polymers1,6638
Water9,746541
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-60 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.326, 131.326, 88.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 21486.764 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus (archaea)
References: UniProt: P43410, adenylate kinase

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Non-polymers , 5 types, 549 molecules

#2: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 % PEP 629, 50 mM Magnesium chloride, 0.1M HEPES pH 7.5, 0.01M TbXo4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.64 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.64 Å / Relative weight: 1
ReflectionResolution: 1.96→49.48 Å / Num. obs: 55867 / % possible obs: 99.8 % / Redundancy: 24.9 % / Biso Wilson estimate: 38 Å2 / Rpim(I) all: 0.027 / Net I/σ(I): 23.1
Reflection shellResolution: 1.96→2.07 Å / Rpim(I) all: 0.38

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→48.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2823 5.06 %RANDOM
Rwork0.171 ---
obs0.172 55803 99.8 %-
Displacement parametersBiso mean: 50.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.0291 Å20 Å20 Å2
2---2.0291 Å20 Å2
3---4.0582 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.96→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 76 550 5096
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019308HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0716945HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2155SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1441HARMONIC5
X-RAY DIFFRACTIONt_it9308HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion16.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion630SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10189SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2547 182 4.61 %
Rwork0.219 3768 -
all0.2207 3950 -
obs--97.17 %
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)
10.1606-0.27870.2041.43980.22690.7962-0.0006-0.04560.0512-0.0320.1004-0.2112-0.11580.1185-0.0998-0.1096-0.03250.0189-0.024-0.0477-0.022643.500961.783820.547
21.8254-0.5578-0.78051.68780.3121.9514-0.2001-0.4694-0.08050.31890.2352-0.11530.39160.4534-0.0351-0.08740.1013-0.04180.06250.011-0.166752.196332.810424.7827
31.62710.2344-0.55511.28560.21610.7419-0.0388-0.1108-0.02110.0655-0.00880.10430.0613-0.06410.0477-0.0858-0.0283-0.0018-0.05250.0101-0.066922.591539.112920.4658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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