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- PDB-3sr0: Crystal Structure of the Phosphoryl Transfer Transition State Mim... -

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Basic information

Entry
Database: PDB / ID: 3sr0
TitleCrystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: ADP/AlF4/AMP in the active site
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Phosphoryl Transfer analogue / AlF4 / transferase (Phosphotransferase) / phosphoryl transfer / Nucleotide-binding / Phosphoryl Transfer of nucleotides
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / intracellular membrane-bounded organelle / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / ADENOSINE MONOPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.565 Å
AuthorsCho, Y.-J. / Kern, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The energy landscape of adenylate kinase during catalysis.
Authors: Kerns, S.J. / Agafonov, R.V. / Cho, Y.J. / Pontiggia, F. / Otten, R. / Pachov, D.V. / Kutter, S. / Phung, L.A. / Murphy, P.N. / Thai, V. / Alber, T. / Hagan, M.F. / Kern, D.
History
DepositionJul 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 18, 2015Group: Database references
Revision 1.4Feb 28, 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 / 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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)48,34210
Polymers46,5382
Non-polymers1,8038
Water13,493749
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1715
Polymers23,2691
Non-polymers9024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1715
Polymers23,2691
Non-polymers9024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.950, 69.580, 85.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 23269.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: adk, Aquifex, aq_078 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66490, adenylate kinase

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Non-polymers , 5 types, 757 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 41.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M Sodium Acetate trihydrate pH 5.4, 0.2M Ammonium Acetate, 30% w/v Polyethylene Glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9739 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2011
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9739 Å / Relative weight: 1
ReflectionResolution: 1.565→41.79 Å / Num. all: 56246 / Num. obs: 56098 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.36 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 1.565→1.61 Å / Redundancy: 4.75 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.7 / Num. unique all: 7959 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
PHENIX(phenix.refine: dev_794)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.565→41.786 Å / SU ML: 0.43 / Isotropic thermal model: anisotropic/isotropic / σ(F): 1.34 / Phase error: 17.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 2844 5.08 %RANDOM
Rwork0.148 ---
obs0.1496 56016 99.57 %-
all-56018 --
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.12 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.474 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6227 Å20 Å2-0 Å2
2--0.4968 Å2-0 Å2
3----1.1195 Å2
Refinement stepCycle: LAST / Resolution: 1.565→41.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 112 749 4097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143608
X-RAY DIFFRACTIONf_angle_d1.5154910
X-RAY DIFFRACTIONf_dihedral_angle_d16.4521452
X-RAY DIFFRACTIONf_chiral_restr0.083534
X-RAY DIFFRACTIONf_plane_restr0.009630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.565-1.5920.26931370.20352530253096
1.592-1.62090.22921280.18052614261498
1.6209-1.65210.27251400.19112619261999
1.6521-1.68590.23131500.170726012601100
1.6859-1.72250.21451520.152626092609100
1.7225-1.76260.20191370.136126342634100
1.7626-1.80670.19351410.132926532653100
1.8067-1.85550.18681350.128426412641100
1.8555-1.91010.19331260.124926602660100
1.9101-1.97180.20031350.131426582658100
1.9718-2.04220.19661610.136226642664100
2.0422-2.1240.16851410.13826482648100
2.124-2.22070.18561290.140726472647100
2.2207-2.33770.17381740.125926522652100
2.3377-2.48420.18521290.127926792679100
2.4842-2.67590.17121380.141926942694100
2.6759-2.94520.17611370.146126702670100
2.9452-3.37120.18531280.148727332733100
3.3712-4.24670.16711560.141827172717100
4.2467-41.80060.19271700.182128492849100

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