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- PDB-2rh5: Structure of Apo Adenylate Kinase from Aquifex Aeolicus -

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Basic information

Entry
Database: PDB / ID: 2rh5
TitleStructure of Apo Adenylate Kinase from Aquifex Aeolicus
ComponentsAdenylate kinase
KeywordsTRANSFERASE / TRANSFERASE(PHOSPHOTRANSFERASE) / ATP-binding / Cytoplasm / Kinase / Nucleotide-binding
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / phosphorylation / intracellular membrane-bounded organelle / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain superfamily / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.48 Å
AuthorsThai, V. / Wolf-Watz, M. / Fenn, T. / Pozharski, E. / Wilson, M.A. / Petsko, G.A. / Kern, D.
CitationJournal: Nature / Year: 2007
Title: Intrinsic motions along an enzymatic reaction trajectory.
Authors: Henzler-Wildman, K.A. / Thai, V. / Lei, M. / Ott, M. / Wolf-Watz, M. / Fenn, T. / Pozharski, E. / Wilson, M.A. / Petsko, G.A. / Karplus, M. / Hubner, C.G. / Kern, D.
History
DepositionOct 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase
C: Adenylate kinase
B: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)69,8073
Polymers69,8073
Non-polymers00
Water45025
1
A: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)23,2691
Polymers23,2691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)23,2691
Polymers23,2691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)23,2691
Polymers23,2691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.681, 157.596, 84.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 23269.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: adk / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: O66490, adenylate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 28-30% (w/v) PEG 3000, 200 mM sodium acetate, and 100 mM TRIS, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 24570 / % possible obs: 96.4 % / Rmerge(I) obs: 0.076 / Χ2: 1.147 / Net I/σ(I): 9.9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.885 / Num. unique all: 2455 / Χ2: 1.285 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
RefinementResolution: 2.48→47.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 23.446 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.735 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1096 4.8 %RANDOM
Rwork0.197 ---
obs0.2 22909 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.48→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 0 25 4867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224938
X-RAY DIFFRACTIONr_angle_refined_deg1.2682.0096660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0595603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5624.225213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07815960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3061536
X-RAY DIFFRACTIONr_chiral_restr0.0870.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023654
X-RAY DIFFRACTIONr_nbd_refined0.2070.21951
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.29
X-RAY DIFFRACTIONr_mcbond_it0.4541.53121
X-RAY DIFFRACTIONr_mcangle_it0.76724938
X-RAY DIFFRACTIONr_scbond_it1.34532003
X-RAY DIFFRACTIONr_scangle_it2.314.51722
LS refinement shellResolution: 2.483→2.548 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 67 -
Rwork0.309 1350 -
all-1417 -
obs--82.62 %
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)
12.6523-1.03970.39913.69710.32632.80910.02320.15750.0896-0.17370.0635-0.2117-0.21490.353-0.0867-0.2605-0.04070.0533-0.194-0.0088-0.229310.659314.73212.598
22.6834-0.102-0.02422.70131.25646.8452-0.1502-0.0246-0.26970.20030.1344-0.42880.37840.38030.0158-0.13970.0518-0.021-0.16430.0124-0.021255.867116.640835.761
33.73511.986-0.60415.6066-1.2963.8410.4424-1.02420.2670.9853-0.29940.4821-0.5749-0.4922-0.14310.2561-0.06090.02850.3481-0.07170.082632.86128.061867.2246
411.19122.2218-0.40613.07790.08552.0520.1133-0.6038-0.0730.3203-0.14310.2222-0.2129-0.35290.0298-0.1160.06060.0423-0.17030.0046-0.1632-13.276721.13467.8101
52.4206-1.5142-0.555113.5456-4.30872.66260.30470.20560.242-1.2363-0.025-0.07940.08610.2391-0.27970.1648-0.0039-0.08930.0202-0.10070.026654.85439.487440.4784
610.18981.76094.05163.57021.03384.02720.0733-0.0336-0.5044-0.04990.0605-0.63120.14380.4711-0.1338-0.0553-0.0662-0.0056-0.04370.01160.051523.0379.790154.1136
74.67551.2228-1.54824.77040.57345.6629-0.1189-0.0014-0.22290.1913-0.02130.07920.2353-0.00330.1402-0.26460.0195-0.0111-0.1579-0.008-0.17368.68217.581923.4668
815.48010.5931-1.87354.23480.5935.6011-0.16720.29471.1549-0.25290.06720.7885-0.5257-0.16020.1-0.0944-0.0551-0.0208-0.02250.05750.108635.152422.428334.3829
95.61482.6869-2.524.92361.947710.2680.08960.74920.5665-0.0366-0.2250.4166-0.8795-1.25380.13540.08870.0779-0.08150.1477-0.02520.137935.969535.626547.2493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 291 - 29
2X-RAY DIFFRACTION1AA72 - 11072 - 110
3X-RAY DIFFRACTION1AA170 - 202170 - 202
4X-RAY DIFFRACTION2CB1 - 291 - 29
5X-RAY DIFFRACTION2CB72 - 11072 - 110
6X-RAY DIFFRACTION2CB170 - 202170 - 202
7X-RAY DIFFRACTION3BC1 - 291 - 29
8X-RAY DIFFRACTION3BC72 - 11072 - 110
9X-RAY DIFFRACTION3BC170 - 202170 - 202
10X-RAY DIFFRACTION4AA111 - 169111 - 169
11X-RAY DIFFRACTION5CB111 - 169111 - 169
12X-RAY DIFFRACTION6BC111 - 169111 - 169
13X-RAY DIFFRACTION7AA30 - 7130 - 71
14X-RAY DIFFRACTION8CB30 - 7130 - 71
15X-RAY DIFFRACTION9BC30 - 7130 - 71

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