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- PDB-6rze: Crystal structure of E. coli Adenylate kinase R119A mutant -

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Basic information

Entry
Database: PDB / ID: 6rze
TitleCrystal structure of E. coli Adenylate kinase R119A mutant
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ADENYLATE KINASE / R119A VARIANT
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 / cytosol / cytoplasm
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
Adenylate kinase / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsGrundstrom, C. / Rogne, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2019
Title: Nucleation of an Activating Conformational Change by a Cation-pi Interaction.
Authors: Rogne, P. / Andersson, D. / Grundstrom, C. / Sauer-Eriksson, E. / Linusson, A. / Wolf-Watz, M.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)23,6746
Polymers23,5341
Non-polymers1405
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-27 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.314, 31.503, 53.189
Angle α, β, γ (deg.)90.00, 110.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-576-

HOH

31A-651-

HOH

41A-652-

HOH

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Components

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


Mass: 23533.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: adk, D9E35_07195, D9H53_18240, D9H70_06005, D9I87_03740, EB509_06410, EB510_02065, EB515_08900, EC382_09075, ED225_07155, ED607_06260, ED611_06205, ED903_02730, ED944_09135, EEA45_02410, EF173_ ...Gene: adk, D9E35_07195, D9H53_18240, D9H70_06005, D9I87_03740, EB509_06410, EB510_02065, EB515_08900, EC382_09075, ED225_07155, ED607_06260, ED611_06205, ED903_02730, ED944_09135, EEA45_02410, EF173_11005, EIA21_12240, NCTC10444_03756, NCTC9112_04001, NCTC9119_03910, NCTC9969_03944, SAMEA3472056_03545, SAMEA3485101_03900, SAMEA3485113_01288
Production host: Escherichia coli (E. coli)
References: UniProt: A0A234NPI7, UniProt: P69441*PLUS, adenylate kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PURIFIED ADK IN 50 MM NACL AND 30 MM MES BUFFER, PH 6.0 WAS CONCENTRATED TO 18 MG/ML AND CO- CRYSTALLIZED WITH A 5 MOLAR EXCESS OF AP5A. A TYPICAL DROP CONTAINED 2 MICROL OF PROTEIN MIXED ...Details: PURIFIED ADK IN 50 MM NACL AND 30 MM MES BUFFER, PH 6.0 WAS CONCENTRATED TO 18 MG/ML AND CO- CRYSTALLIZED WITH A 5 MOLAR EXCESS OF AP5A. A TYPICAL DROP CONTAINED 2 MICROL OF PROTEIN MIXED WITH 2 MICROL OF PRECIPITANT AND EQUILIBRATED AGAINST 1 ML RESERVOIR SOLUTION CONTAINING 28-30% PEG 4K, 0.2 M MgCL2 AND 0.1 M Tris-HCl, PH 8.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.69→48.221 Å / Num. obs: 22857 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.09 / Net I/σ(I): 7.2
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2087 / CC1/2: 0.598 / Rpim(I) all: 0.568

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x8h

4x8h


Resolution: 1.69→48.221 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.52
RfactorNum. reflection% reflection
Rfree0.235 1915 8.38 %
Rwork0.1819 --
obs0.1865 22857 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.69→48.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 5 355 2009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061701
X-RAY DIFFRACTIONf_angle_d0.8632297
X-RAY DIFFRACTIONf_dihedral_angle_d12.8471054
X-RAY DIFFRACTIONf_chiral_restr0.05258
X-RAY DIFFRACTIONf_plane_restr0.005304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.73230.36321170.26961350X-RAY DIFFRACTION87
1.7323-1.77910.3531220.26061395X-RAY DIFFRACTION90
1.7791-1.83150.30441330.24271413X-RAY DIFFRACTION91
1.8315-1.89060.29141220.23551413X-RAY DIFFRACTION94
1.8906-1.95820.26971370.21781478X-RAY DIFFRACTION95
1.9582-2.03660.29621340.19981484X-RAY DIFFRACTION96
2.0366-2.12920.25671360.18861507X-RAY DIFFRACTION98
2.1292-2.24150.23021460.17541530X-RAY DIFFRACTION99
2.2415-2.38190.22131360.1651522X-RAY DIFFRACTION99
2.3819-2.56580.21381430.17341546X-RAY DIFFRACTION100
2.5658-2.8240.25621450.18641556X-RAY DIFFRACTION100
2.824-3.23260.22291430.17521546X-RAY DIFFRACTION99
3.2326-4.07240.20061470.14881575X-RAY DIFFRACTION100
4.0724-48.24070.20081540.16931627X-RAY DIFFRACTION100

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