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- PDB-4jzk: Crystal Structure of Adenylate kinase of E. Coli with ADP/AMP bound -

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Basic information

Entry
Database: PDB / ID: 4jzk
TitleCrystal Structure of Adenylate kinase of E. Coli with ADP/AMP bound
ComponentsAdenylate kinase
KeywordsTRANSFERASE / phosphoryl transfer reaction / conformational changes of lids domains / ATP binding / AMP binding / phosphoryl transfer
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli O104:H4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsCho, Y.-J. / Agafonov, R. / Kern, D.
CitationJournal: To be Published
Title: Crystal structure of E. Coli Adenylate kinase with ADP and AMP bound
Authors: Cho, Y.-J. / Agafonov, R. / Kern, D.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)48,7896
Polymers47,2402
Non-polymers1,5494
Water12,556697
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3943
Polymers23,6201
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3943
Polymers23,6201
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.960, 78.800, 83.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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


Mass: 23620.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O104:H4 (bacteria) / Strain: 2009EL-2071 / Gene: adk, O3O_06175 / Production host: Escherichia coli (E. coli) / References: UniProt: K0BFA4, adenylate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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 / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 2.3 M ammonium sulfate and 100 mM imidazole at pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.63→26.11 Å / Num. obs: 58505 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 5.6
Reflection shellResolution: 1.63→1.72 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.5 / % possible all: 82

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→25.883 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 0 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 2864 5.06 %
Rwork0.2145 --
obs0.2164 56588 93.7 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.785 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4054 Å2-0 Å20 Å2
2---1.8673 Å2-0 Å2
3---5.2727 Å2
Refinement stepCycle: LAST / Resolution: 1.63→25.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 100 697 4109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073468
X-RAY DIFFRACTIONf_angle_d1.1814694
X-RAY DIFFRACTIONf_dihedral_angle_d16.8411344
X-RAY DIFFRACTIONf_chiral_restr0.066524
X-RAY DIFFRACTIONf_plane_restr0.005602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.68830.34832300.32253965X-RAY DIFFRACTION71
1.6883-1.75580.34182490.29124910X-RAY DIFFRACTION87
1.7558-1.83570.31083050.2735470X-RAY DIFFRACTION96
1.8357-1.93250.40052600.32475145X-RAY DIFFRACTION90
1.9325-2.05350.28212730.2255536X-RAY DIFFRACTION97
2.0535-2.2120.24532730.21075719X-RAY DIFFRACTION100
2.212-2.43440.30263450.24015503X-RAY DIFFRACTION97
2.4344-2.78630.23943120.20055730X-RAY DIFFRACTION100
2.7863-3.50910.22452840.1955778X-RAY DIFFRACTION100
3.5091-25.88620.19843330.17695968X-RAY DIFFRACTION99
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)
13.9049-0.26891.14320.6242-0.59240.7521-0.0954-0.10490.6657-0.1001-0.0221-0.0864-0.04560.1377-0.10720.0617-0.0096-0.02720.1284-0.06310.0676-15.845910.7113-12.1189
22.13250.1082-1.08550.5982-0.47350.64070.1251-0.25390.1722-0.0123-0.101-0.1577-0.09510.11840.04810.0618-0.0114-0.03550.1721-0.01150.0082-3.85715.2967-16.1773
30.6941-0.49930.54271.0938-0.8340.6029-0.11040.05110.1009-0.10750.05940.0307-0.0137-0.02820.04050.113-0.0067-0.03870.1215-0.00170.0742-19.44228.5089-28.2667
41.14460.63130.12751.2417-0.15830.01630.0901-0.3538-0.0310.0684-0.06790.06570.0323-0.01720.00620.0487-0.0226-0.0040.1862-0.01980.0027-18.10950.6236-8.6553
50.60190.219-0.53991.5245-0.16360.52980.2177-0.28970.4519-0.037-0.05731.0458-0.1168-0.0573-0.12760.17960.01080.01080.04340.00550.5777-26.404445.4252-24.7357
60.4930.3735-0.08860.60350.1770.753-0.29310.33060.5085-0.80390.13011.2972-0.1353-0.18690.08680.4088-0.0248-0.32410.12390.12890.8478-28.102740.8542-34.0845
70.62790.27220.36830.91820.19880.14320.0702-0.2485-0.2676-0.0014-0.0831-0.00870.0888-0.09240.00190.2067-0.03880.02130.11150.01920.2546-12.699651.2264-18.7289
81.33880.7585-0.31542.5521-0.49120.99180.1178-0.0359-0.2178-0.4697-0.07870.21020.19790.1241-0.01480.23640.0421-0.02010.05190.04850.3554-16.069835.9004-28.4285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:26)
2X-RAY DIFFRACTION2(chain A and resid 27:110)
3X-RAY DIFFRACTION3(chain A and resid 111:168)
4X-RAY DIFFRACTION4(chain A and resid 169:214)
5X-RAY DIFFRACTION5(chain B and resid 1:69)
6X-RAY DIFFRACTION6(chain B and resid 70:109)
7X-RAY DIFFRACTION7(chain B and resid 110:158)
8X-RAY DIFFRACTION8(chain B and resid 159:214)

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