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- PDB-1e4y: Mutant P9L of adenylate kinase from E. coli, modified in the Gly-loop -

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Basic information

Entry
Database: PDB / ID: 1e4y
TitleMutant P9L of adenylate kinase from E. coli, modified in the Gly-loop
ComponentsAdenylate kinase
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding ...purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium 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, 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMueller, C.W. / Schulz, G.E.
Citation
Journal: Proteins / Year: 1993
Title: Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop.
Authors: Muller, C.W. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Induced-Fit Movements in Adenylate Kinases
Authors: Schulz, G.E. / Mueller, C.W. / Diederichs, K.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of the Complex of Adenylate Kinase from Escherichia Coli with the Inhibitor P1, P5-Bis (Adenosine-5'-) Pentaphosphate
Authors: Mueller, C.W. / Schulz, G.E.
History
DepositionJul 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 21, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)49,1894
Polymers47,3562
Non-polymers1,8332
Water00
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5952
Polymers23,6781
Non-polymers9161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5952
Polymers23,6781
Non-polymers9161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.300, 77.800, 57.700
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.995341, 0.068333, 0.068023), (0.038108, 0.92686, -0.373469), (-0.088568, -0.369136, -0.925145)
Vector: 38.70362, 47.46029, 42.28705)

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Components

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


Mass: 23678.150 Da / Num. of mol.: 2 / Mutation: L9P
Source method: isolated from a genetically manipulated source
Details: AP5A / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CV2 / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
Compound detailsCHAIN A, B ENGINEERED MUTATION PRO9LEU

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growpH: 7.2 / Details: pH 7.20
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-25 mg/mlprotein1drop
22 mMAp5A1drop
350 mMMES1drop
41.5 %(w/v)PEG15001drop
51.5 Mammonium sulfate1drop
650 mMMES1reservoir
72.0-2.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→10 Å / Num. obs: 7261 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1

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Processing

Software
NameVersionClassification
X-PLOR1.5refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.178 --
obs0.178 7261 90 %
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 114 0 3428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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