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- PDB-4qbh: Crystal structure of a stable adenylate kinase variant AKlse5 -

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Basic information

Entry
Database: PDB / ID: 4qbh
TitleCrystal structure of a stable adenylate kinase variant AKlse5
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Adenylate kinase / Zinc finger / transferase activity / phosphotransferase activity / Zinc binding / ATP binding / Phosphorylation
Function / homology
Function and homology information


adenylate kinase / adenylate kinase activity / AMP salvage / phosphorylation / 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 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...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 / 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 speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8928
Polymers48,8802
Non-polymers2,0126
Water7,224401
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4464
Polymers24,4401
Non-polymers1,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4464
Polymers24,4401
Non-polymers1,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.089, 75.360, 81.982
Angle α, β, γ (deg.)90.00, 89.996, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24440.090 Da / Num. of mol.: 2 / Mutation: 34 mutations
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: 168 / Gene: adk / Production host: Escherichia coli (E. coli) / References: UniProt: P27142, adenylate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26.5% (w/v) polyethylene glycol 4000, 150mM magnesium acetate, 100mM sodium cacodylate pH 6.5, 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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 9, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.67→81.98 Å / Num. all: 50674 / Num. obs: 49458 / % possible obs: 97.6 %
Reflection shellResolution: 1.68→1.74 Å / % possible all: 95.7

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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: 1ZIN

1zin


Resolution: 1.67→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.605 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22327 2516 5.1 %RANDOM
Rwork0.17628 ---
obs0.17868 46923 96.99 %-
all-48379 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å2-0.46 Å2
2---1.03 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 1.67→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 118 401 3912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193569
X-RAY DIFFRACTIONr_bond_other_d0.0010.023402
X-RAY DIFFRACTIONr_angle_refined_deg2.1992.0294831
X-RAY DIFFRACTIONr_angle_other_deg0.94637825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93623.988173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.415635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8521535
X-RAY DIFFRACTIONr_chiral_restr0.1210.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_mcbond_it1.4631.521726
X-RAY DIFFRACTIONr_mcbond_other1.4621.5181725
X-RAY DIFFRACTIONr_mcangle_it2.1362.2742154
X-RAY DIFFRACTIONr_mcangle_other2.1362.2762155
X-RAY DIFFRACTIONr_scbond_it2.7481.8441843
X-RAY DIFFRACTIONr_scbond_other2.7471.8441844
X-RAY DIFFRACTIONr_scangle_other4.1712.6282678
X-RAY DIFFRACTIONr_long_range_B_refined7.49514.2664451
X-RAY DIFFRACTIONr_long_range_B_other7.39813.4434276
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 164 -
Rwork0.265 3106 -
obs--87.2 %
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)
10.83160.10.99370.6356-0.4952.9538-0.0480.00070.14820.00420.00020.05210.0205-0.13410.04780.0490.0127-0.00950.03110.00310.088-13.4081-8.1537-24.953
21.86950.27912.10240.12920.55633.50920.0229-0.2339-0.06250.0082-0.07960.0060.0821-0.42740.05660.0123-0.00970.01840.0567-0.01180.0447-19.087-26.9857-20.6893
30.5678-0.00320.28290.39710.03271.1722-0.0138-0.03140.06350.06780.0056-0.0083-0.0537-0.01930.00820.0428-0.00360.02530.0193-0.02230.0448-6.7076-14.8931-9.3297
40.643-0.08160.350.05030.09141.5380.01340.0392-0.00140.00070.0179-0.0072-0.01890.0858-0.03130.0725-0.01140.02110.0181-0.01210.043-9.0514-19.619-17.4111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 60
2X-RAY DIFFRACTION1B31 - 60
3X-RAY DIFFRACTION2A127 - 164
4X-RAY DIFFRACTION2B127 - 164
5X-RAY DIFFRACTION3A1 - 30
6X-RAY DIFFRACTION3B1 - 30
7X-RAY DIFFRACTION3A61 - 126
8X-RAY DIFFRACTION3B61 - 126
9X-RAY DIFFRACTION3A165 - 217
10X-RAY DIFFRACTION3B165 - 214
11X-RAY DIFFRACTION4A301
12X-RAY DIFFRACTION4B301

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