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- PDB-4qbf: Crystal structure of a stable adenylate kinase variant AKlse2 -

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Basic information

Entry
Database: PDB / ID: 4qbf
TitleCrystal structure of a stable adenylate kinase variant AKlse2
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Adenylate kinase / Zinc finger / phosphotransferase activity / Zinc binding / ATP binding / Phosphorylation
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 / zinc ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP 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 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP 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 speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMoon, S. / Bae, E.
CitationJournal: Proteins / Year: 2014
Title: Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases.
Authors: Moon, S. / Bannen, R.M. / Rutkoski, T.J. / Phillips Jr., G.N. / Bae, E.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0523
Polymers24,0711
Non-polymers9822
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.293, 47.202, 109.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP/AMP phosphotransferase / Adenylate monophosphate kinase / ...AK / ATP-AMP transphosphorylase / ATP/AMP phosphotransferase / Adenylate monophosphate kinase / Superoxide-inducible protein 16 / SOI16


Mass: 24070.535 Da / Num. of mol.: 1 / Mutation: 26 mutations
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: adk, BSU01370 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P16304, 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.: 144 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.9M ammonium citrate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 19437 / Num. obs: 19418 / % possible obs: 99.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MKG

4mkg


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.774 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22247 992 5.1 %RANDOM
Rwork0.17125 ---
obs0.17382 18376 99.62 %-
all-18446 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.634 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2---0.07 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 58 144 1876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191761
X-RAY DIFFRACTIONr_bond_other_d0.0010.021689
X-RAY DIFFRACTIONr_angle_refined_deg2.3312.0362389
X-RAY DIFFRACTIONr_angle_other_deg2.55133903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7485215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27825.06577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94915316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1651512
X-RAY DIFFRACTIONr_chiral_restr0.1320.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211937
X-RAY DIFFRACTIONr_gen_planes_other0.010.02357
X-RAY DIFFRACTIONr_mcbond_it1.7451.64863
X-RAY DIFFRACTIONr_mcbond_other1.7051.638862
X-RAY DIFFRACTIONr_mcangle_it2.4692.451077
X-RAY DIFFRACTIONr_mcangle_other2.4732.4521078
X-RAY DIFFRACTIONr_scbond_it3.1682.128898
X-RAY DIFFRACTIONr_scbond_other3.1672.128899
X-RAY DIFFRACTIONr_scangle_other53.0391313
X-RAY DIFFRACTIONr_long_range_B_refined7.40315.2872101
X-RAY DIFFRACTIONr_long_range_B_other7.35414.7732053
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 86 -
Rwork0.207 1249 -
obs-100 96.25 %
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)
11.7693-0.4332-1.27374.216-0.58972.6337-0.1439-0.1521-0.00870.03880.10910.1090.1081-0.07690.03470.0508-0.02250.01880.0826-0.01020.0167-15.6745-2.702-5.8734
20.9614-0.01271.11021.57831.95253.74340.0278-0.16830.09240.00240.0433-0.14210.0601-0.1234-0.07110.05610.00210.01550.0591-0.01880.02434.72893.9966-0.9397
30.77990.35650.20041.2430.30630.82770.02730.01940.0815-0.0509-0.07140.15040.0203-0.05490.04410.00960.0026-0.00160.014-0.00760.0216-8.33316.6233-20.2595
40000000000000000.0304000.030400.0304-3.7691.937-12.402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 60
2X-RAY DIFFRACTION2A127 - 164
3X-RAY DIFFRACTION3A1 - 30
4X-RAY DIFFRACTION3A61 - 126
5X-RAY DIFFRACTION3A165 - 216
6X-RAY DIFFRACTION4A302

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