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- PDB-8crg: E. coli adenylate kinase in complex with two ADP molecules as a r... -

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Basic information

Entry
Database: PDB / ID: 8crg
TitleE. coli adenylate kinase in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis
ComponentsAdenylate kinase
KeywordsTRANSFERASE / phosphotransferase / energy metabolism / AP4A hydrolysis / potential moonlighting protein
Function / homology
Function and homology information


purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / phosphorylation ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / phosphorylation / 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 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsOelker, M. / Tischlik, S. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, European Union, 3items
OrganizationGrant numberCountry
Swedish Research Council2021-04513_VR Sweden
European Research Council (ERC)772027-SPICE-ERC-2017-COGEuropean Union
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2023
Title: Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by E. coli Adenylate Kinase.
Authors: Tischlik, S. / Oelker, M. / Rogne, P. / Sauer-Eriksson, A.E. / Drescher, M. / Wolf-Watz, M.
History
DepositionMar 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_validate_planes.type
Revision 1.2Aug 9, 2023Group: Data collection / Database references / Category: citation / pdbx_validate_planes
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_validate_planes.type
Revision 2.0Oct 25, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / entity_poly / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_planes / pdbx_validate_torsion / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id ..._atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _entity_poly.pdbx_strand_id / _pdbx_database_status.pdb_format_compatible / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_validate_planes.auth_asym_id / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_ref_seq.pdbx_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_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)49,1587
Polymers47,2402
Non-polymers1,9185
Water8,863492
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6844
Polymers23,6201
Non-polymers1,0643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4743
Polymers23,6201
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.810, 77.360, 59.600
Angle α, β, γ (deg.)90.000, 95.484, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 23620.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: adk, dnaW, plsA, b0474, JW0463
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P69441, adenylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 % (w/v) PEG 3350, 100 mM Bis-tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.49→37.61 Å / Num. obs: 285900 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Net I/σ(I): 15.31
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 21040 / CC1/2: 0.515 / Rpim(I) all: 0.542 / Rrim(I) all: 1.085 / % possible all: 98.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREP11phasing
Coot0.9.8.6model building
REFMAC5.0.32refinement
PHENIX1.19.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→37.61 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1907 2076 2.5 %
Rwork0.1632 80973 -
obs0.1639 83049 99.19 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.74 Å2
Refinement stepCycle: LAST / Resolution: 1.49→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 121 492 3925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933740
X-RAY DIFFRACTIONf_angle_d1.29675095
X-RAY DIFFRACTIONf_chiral_restr0.0771559
X-RAY DIFFRACTIONf_plane_restr0.0197659
X-RAY DIFFRACTIONf_dihedral_angle_d19.8478580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.29991370.27385359X-RAY DIFFRACTION98.78
1.52-1.560.26481370.26515342X-RAY DIFFRACTION98.93
1.56-1.610.26961380.25465365X-RAY DIFFRACTION98.96
1.61-1.650.26411380.23035395X-RAY DIFFRACTION99.05
1.65-1.710.26731380.21015356X-RAY DIFFRACTION99.19
1.71-1.770.22971380.19265374X-RAY DIFFRACTION99.21
1.77-1.840.1951380.18615418X-RAY DIFFRACTION99.3
1.84-1.920.22861390.18795395X-RAY DIFFRACTION99.53
1.92-2.020.18321380.1745393X-RAY DIFFRACTION99.53
2.02-2.150.18041390.16885421X-RAY DIFFRACTION99.48
2.15-2.310.18121380.15495396X-RAY DIFFRACTION99.41
2.31-2.550.20641390.16165417X-RAY DIFFRACTION99.5
2.55-2.920.19941400.16485446X-RAY DIFFRACTION99.41
2.92-3.670.18671390.15015424X-RAY DIFFRACTION99.22
3.67-37.610.15941400.13755472X-RAY DIFFRACTION98.44
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)
12.330065025530.229497753168-0.5468089506361.7108432359-0.7907737881073.201133098560.115695088176-0.1594875846230.2879729694040.162627806347-0.04277325954480.167893953458-0.285793640765-0.0582627027449-0.07634742072760.1790808729270.006556614040970.008755894522480.144508253051-0.01385734711540.192258533943-22.8984820054.780598193434.43080537297
25.303802573625.05934919879-1.322146505945.268926447560.2929628250245.2236328593-0.4505348487080.370131066036-0.274255699311-0.8512398676640.0727837686275-0.3208356952770.3791642655110.1769331530730.3837038045520.317596228592-0.008111412338130.01267369933350.3524390933520.02366284294180.274707449081-9.387337083940.237894645848-8.98437609919
36.30785761761-1.097832647521.195506844096.284570564512.190173387576.442265022170.00488600908658-0.07312769368110.122183651674-0.156006405290.18360037172-0.535834491428-0.1281835906470.538658888327-0.2148233475510.108599757661-0.006236401162660.02248835228290.146652767370.03035846951930.13485823044-10.5049068-3.033033911082.7622120392
41.48797505533-0.622059570038-0.06893784302492.224809127280.1579885403762.87018503072-0.0685687235267-0.2852796835460.04410640311950.1000116582250.132243738717-0.00779180126078-0.04658340002110.0859725917574-0.061961779030.162290822089-0.007994130409550.01005650878220.177014373111-0.001848590350320.151601848762-19.6527265669-3.1436711311310.6944890925
51.16432316368-2.166477825111.34087724533.31994063047-2.468816704782.507886179510.08446009606590.0505552299380.269240468763-0.324223718367-0.00453787297267-0.0168515819750.08039885982060.0240213119904-0.08490012857360.2404488535550.0237210931609-0.0148800970240.2139716769360.002682841134740.321362073964-29.84742765557.62276009278-8.92831728124
65.371732074480.6185963158140.8683234668357.19692378731-4.971140228137.619292322720.036214442650.400947833843-0.258097619709-0.849191038223-0.0555736682190.05536131731021.107769139320.108855808403-0.006859845012770.316659556683-0.00372237803841-0.0295874714090.203279181009-0.06730234258380.217666212086-25.0172016979-10.4406521828-7.86955141085
72.292430697-1.054196957470.9103056209943.77958914944-1.788358608482.60363619904-0.106319452717-0.164168143226-0.0933322406030.288364132080.2376484349610.413188644775-0.0830155650014-0.453924415323-0.1315199756680.154031477762-0.02388055473140.0448679862120.24900429240.02818609355240.22024918246-31.7451388844-4.803965194711.5656791603
88.14370703637-1.10483604267-2.41299479774.964844009160.374292924773.328632503950.09840089268990.1573431457010.390860010278-0.33964992082-0.1083519775250.130590720485-0.422733998558-0.2115267550470.009679081381780.2475520675630.0372052160588-0.03961396195050.163437441878-0.01432012321570.144202173804-7.695327906922.739235994-28.8515729266
93.279923196151.897826810851.571335741795.17064737572.216827510722.804937046760.1313551228510.0234048255908-0.6396740999270.2749674968020.164312896258-0.5193707663150.09942015997310.265001453008-0.242713575940.144988734632-0.02588821647830.0009350790871930.190067415117-0.01993511832940.2148591896694.166296377822.7269072721-12.2376939529
106.316409440140.05867976531491.743904623086.95251427887-1.011990384043.670500463130.136590132452-0.555470222592-0.1003584378040.380739799048-0.0592348872096-0.394485921195-0.0150830444391-0.00731357017833-0.1380793185930.162113799693-0.05021992423410.01481991384440.213223473151-0.000578044179550.148194871787-3.0865641075515.7893927024-11.1409943797
113.11019393639-0.974596772099-0.1255907602654.49328555417-0.226463790732.262706485430.0530581121741-0.296596505420.1153792227430.0674433907753-0.1163069744320.297127115572-0.125528401589-0.195673412720.04200967488470.1351630289120.002458311222370.01277978499730.204559405682-0.04919365983130.159332248167-10.786108850216.8807667156-17.3173781087
124.421503609550.875188591191-0.7056445471982.11181382248-1.364667538921.755927617080.08197298375920.366539511460.168058691196-0.2463736257490.00632061827270.224053570282-0.174362745829-0.4917958473350.04389786892370.251451140220.0157403921985-0.02393145179120.221718589161-0.04376156754880.198813056454-10.362634093413.5532192564-28.1547915192
132.714191445361.67567154958-0.2566534106474.56654031748-1.029785770652.20775710899-0.04160622521980.0381087682834-0.252321837793-0.2766488351090.0171210004608-0.4602335455990.02035274871230.1399380943390.04901314094910.233598626743-0.03612663892670.06469429096640.2114112513710.0007331229910390.2135188596448.4856890780323.2082627764-30.4724268776
142.751231607260.938522322482-0.9151210649285.30411546258-2.419082797412.238458937160.03534693403150.0516192508176-0.182425935764-0.0889073176303-0.172624591441-0.463509999107-0.0378169542560.1678234629940.1341906225040.243179855764-0.04369574597530.04049247920030.22581470461-0.005015108337830.228629343211.838849165329.7336674219-29.5750078422
155.741534729762.22424865927-0.74665119640.871342839669-0.3101464567550.167051841965-0.260735269414-0.213981127403-1.01199793351-0.802708139527-0.627757545484-2.574251774860.3417534037250.5838687275980.2388812996610.2753516975450.125160310210.2094561402020.3210254717660.2147470063930.9348661751898.927628333798.76200278327-24.0203594557
162.34838427634-0.1115081918043.261388681974.04174243232-0.7169775811874.889028029460.104587862641-0.0684404232503-0.348033105322-0.261617362799-0.1706966257720.2754201809260.371391764678-0.2456501434440.04163743726660.2521948549640.003053730164350.03853981934240.20233121399-0.04563420721160.223072770917-10.27841783265.09744552813-25.8508731238
175.151015481223.77834001483-2.675857891256.39865697301-2.284650861053.95521359322-0.08453886208080.4578286680770.175974274166-0.6026097925060.01074600188330.388299344851-0.10574968425-0.3584923633650.05327442035280.3231493288340.0260254027537-0.07655510298090.337105960736-0.01587571719150.201205299401-9.7561709546517.3117075196-36.6795254682
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11{ A|1-41 }AA1 - 411 - 41
22{ A|42-54 }AA42 - 5442 - 54
33{ A|55-73 }AA55 - 7355 - 73
44{ A|74-112 }AA74 - 11274 - 112
55{ A|113-160 }AA113 - 160113 - 160
66{ A|161-174 }AA161 - 174161 - 174
77{ A|175-214 }AA175 - 214175 - 214
88{ B|1-26 }BB1 - 261 - 26
99{ B|27-55 }BB27 - 5527 - 55
1010{ B|56-72 }BB56 - 7256 - 72
1111{ B|73-98 }BB73 - 9873 - 98
1212{ B|99-112 }BB99 - 11299 - 112
1313{ B|113-134 }BB113 - 134113 - 134
1414{ B|135-160 }BB135 - 160135 - 160
1515{ B|161-174 }BB161 - 174161 - 174
1616{ B|175-187 }BB175 - 187175 - 187
1717{ B|188-214 }BB188 - 214188 - 214

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