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- PDB-4w5j: New structural conformations of adenylate kinase from Streptococc... -

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Basic information

Entry
Database: PDB / ID: 4w5j
TitleNew structural conformations of adenylate kinase from Streptococcus pneumoniae D39 with Ap5A
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase / NMP/LID domain / AMP/ATP binding / phosphotransferase
Function / homology
Function and homology information


CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / cytosol
Similarity search - Function
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 speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsThach, T.T. / Lee, S.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations.
Authors: Thach, T.T. / Lee, S.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
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
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_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_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.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

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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
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,38412
Polymers96,6214
Non-polymers3,7638
Water14,592810
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0963
Polymers24,1551
Non-polymers9412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0963
Polymers24,1551
Non-polymers9412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0963
Polymers24,1551
Non-polymers9412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0963
Polymers24,1551
Non-polymers9412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.908, 62.298, 63.022
Angle α, β, γ (deg.)101.89, 112.59, 89.86
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 24155.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria)
Gene: adk, SPD_0214 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04ML5, adenylate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 810 / 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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 Sodium acetate, 0.1M Sodium acetate pH 4.6, 30%(v/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 13, 2011
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→46.99 Å / Num. obs: 85180 / % possible obs: 95.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 39.02
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.43 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NU0

4nu0


Resolution: 1.65→46.99 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 37.78
RfactorNum. reflection% reflection
Rfree0.286 4265 5.03 %
Rwork0.257 --
obs0.258 84865 95.4 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.26 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 232 810 7682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066988
X-RAY DIFFRACTIONf_angle_d1.1469488
X-RAY DIFFRACTIONf_dihedral_angle_d15.5712696
X-RAY DIFFRACTIONf_chiral_restr0.0381064
X-RAY DIFFRACTIONf_plane_restr0.0041208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6492-1.66790.3391240.34382486X-RAY DIFFRACTION89
1.6679-1.68750.34281460.31712665X-RAY DIFFRACTION94
1.6875-1.70810.3331250.31182672X-RAY DIFFRACTION95
1.7081-1.72970.36491380.31552701X-RAY DIFFRACTION94
1.7297-1.75250.3491480.32512668X-RAY DIFFRACTION96
1.7525-1.77650.36331430.30992656X-RAY DIFFRACTION95
1.7765-1.80190.31571660.29982721X-RAY DIFFRACTION96
1.8019-1.82880.31011380.29612651X-RAY DIFFRACTION95
1.8288-1.85740.32051460.30932688X-RAY DIFFRACTION96
1.8574-1.88780.30951290.28982702X-RAY DIFFRACTION95
1.8878-1.92040.32891480.30252736X-RAY DIFFRACTION97
1.9204-1.95530.34341550.28142659X-RAY DIFFRACTION96
1.9553-1.99290.34161490.28892717X-RAY DIFFRACTION97
1.9929-2.03360.30651330.2762739X-RAY DIFFRACTION97
2.0336-2.07780.32281440.27412744X-RAY DIFFRACTION96
2.0778-2.12610.33151520.26452684X-RAY DIFFRACTION97
2.1261-2.17930.29721320.26392748X-RAY DIFFRACTION97
2.1793-2.23820.30961340.26482723X-RAY DIFFRACTION96
2.2382-2.30410.29971430.25712746X-RAY DIFFRACTION97
2.3041-2.37840.30151580.25592695X-RAY DIFFRACTION97
2.3784-2.46340.31861400.262741X-RAY DIFFRACTION97
2.4634-2.56210.2481370.24692773X-RAY DIFFRACTION97
2.5621-2.67870.28111310.25882754X-RAY DIFFRACTION98
2.6787-2.81990.28111540.25722773X-RAY DIFFRACTION98
2.8199-2.99650.26861630.25662747X-RAY DIFFRACTION98
2.9965-3.22780.23481560.22852708X-RAY DIFFRACTION98
3.2278-3.55250.271530.22082726X-RAY DIFFRACTION97
3.5525-4.06640.22481430.21452657X-RAY DIFFRACTION94
4.0664-5.12220.2691190.22832538X-RAY DIFFRACTION89
5.1222-47.01160.31451180.28152382X-RAY DIFFRACTION84

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