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- PDB-5x6j: Crystal structure of B. globisporus adenylate kinase variant -

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Basic information

Entry
Database: PDB / ID: 5x6j
TitleCrystal structure of B. globisporus adenylate kinase variant
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ATP binding / phosphotransferase activity
Function / homology
Function and homology information


adenylate kinase / AMP kinase activity / AMP salvage / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / 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 ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / 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
Similarity search - Component
Biological speciesSporosarcina globispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMoon, S. / Bae, E.
CitationJournal: Struct Dyn. / Year: 2019
Title: Structural and mutational analyses of psychrophilic and mesophilic adenylate kinases highlight the role of hydrophobic interactions in protein thermal stability.
Authors: Moon, S. / Kim, J. / Koo, J. / Bae, E.
History
DepositionFeb 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9103
Polymers23,9281
Non-polymers9822
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-1 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.106, 65.106, 94.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 23928.262 Da / Num. of mol.: 1 / Fragment: T26I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporosarcina globispora (bacteria) / Gene: adk / Production host: Escherichia coli (E. coli) / References: UniProt: P84139, adenylate kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 2.5M ammonium sulfate, 1% polyethylene glycol 1000, 0.1% Sodium azide, 50mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13990 / % possible obs: 99.8 % / Redundancy: 21.6 % / Net I/σ(I): 53.98
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 21.9 % / Rmerge(I) obs: 0.508 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3G

1s3g


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.546 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.219 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27611 683 4.9 %RANDOM
Rwork0.1931 ---
obs0.19679 13143 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.319 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 58 89 1795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191732
X-RAY DIFFRACTIONr_bond_other_d0.0010.021662
X-RAY DIFFRACTIONr_angle_refined_deg2.0432.0242350
X-RAY DIFFRACTIONr_angle_other_deg0.88133832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0775212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41425.44379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24415309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4651511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2443.796851
X-RAY DIFFRACTIONr_mcbond_other3.2353.793850
X-RAY DIFFRACTIONr_mcangle_it4.2995.6711062
X-RAY DIFFRACTIONr_mcangle_other4.2995.6751063
X-RAY DIFFRACTIONr_scbond_it3.844.143881
X-RAY DIFFRACTIONr_scbond_other3.8384.143882
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6986.0521289
X-RAY DIFFRACTIONr_long_range_B_refined7.31230.5622023
X-RAY DIFFRACTIONr_long_range_B_other7.31330.391995
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 52 -
Rwork0.261 951 -
obs--99.9 %
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)
10.5291-0.3156-0.15921.21610.50892.03150.04480.02730.16640.1780.0135-0.1290.32030.1608-0.05830.1076-0.01280.01370.0684-0.0040.0558-13.741312.3222-5.3963
21.69230.43441.29053.37-0.19562.087-0.11450.0960.1647-0.12650.0006-0.1457-0.1962-0.07290.11380.099-0.0283-0.00440.05270.01480.0381-20.389623.8746-18.2612
30.2988-0.34890.03291.64241.56952.10280.01090.05010.00990.0436-0.15180.08010.0064-0.15660.1410.0959-0.06040.04020.0949-0.01720.0278-25.143428.8261.5032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION1A61 - 126
3X-RAY DIFFRACTION1A165 - 213
4X-RAY DIFFRACTION2A31 - 60
5X-RAY DIFFRACTION3A127 - 164

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