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- PDB-2gl0: Structure of PAE2307 in complex with adenosine -

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Basic information

Entry
Database: PDB / ID: 2gl0
TitleStructure of PAE2307 in complex with adenosine
Componentsconserved hypothetical protein
KeywordsTRANSFERASE / histidine phosphorylation / putative kinase / protein-adenosine complex
Function / homology
Function and homology information


Ta1353-like / Adenosine specific kinase / Ta1353-like superfamily / Adenosine specific kinase / hypothetical protein tt1634 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / PHOSPHATE ION / Adenosine monophosphate-protein transferase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLott, J.S. / Paget, B. / Johnston, J.M. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Structure of an Ancient Conserved Domain Establishes a Structural Basis for Stable Histidine Phosphorylation and Identifies a New Family of Adenosine-specific Kinases.
Authors: Lott, J.S. / Paget, B. / Johnston, J.M. / Delbaere, L.T. / Sigrell-Simon, J.A. / Banfield, M.J. / Baker, E.N.
History
DepositionApr 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein
D: conserved hypothetical protein
E: conserved hypothetical protein
F: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,81214
Polymers112,0196
Non-polymers1,7938
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33200 Å2
ΔGint-70 kcal/mol
Surface area28830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.862, 109.825, 112.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
conserved hypothetical protein


Mass: 18669.756 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: IM2 / Gene: PAE2307 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZVF7, adenosine kinase
#2: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 21% (w/v) MPEG 5000, 0.2M AMPSO/KOH, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2005 / Details: silicon monochromator
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.25→112.509 Å / Num. obs: 45062 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 7.8
Reflection shellResolution: 2.25→2.37 Å / % possible obs: 94.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3 / Num. measured all: 19415 / Num. unique all: 6169 / Num. unique obs: 6169 / Rsym value: 0.238 / % possible all: 94.6

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Phasing

Phasing MRRfactor: 0.434 / Cor.coef. Fo:Fc: 0.599
Highest resolutionLowest resolution
Rotation4 Å49.35 Å
Translation4 Å49.35 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WVQ

1wvq


Resolution: 2.25→49.33 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.497 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2273 5 %RANDOM
Rwork0.17 ---
all0.174 45951 --
obs-45058 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.323 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7686 0 124 407 8217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0227960
X-RAY DIFFRACTIONr_angle_refined_deg2.2971.9910804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2155970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75423.86342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.896151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2461560
X-RAY DIFFRACTIONr_chiral_restr0.1510.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025872
X-RAY DIFFRACTIONr_nbd_refined0.2340.23670
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25286
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2502
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.26
X-RAY DIFFRACTIONr_mcbond_it1.0411.55089
X-RAY DIFFRACTIONr_mcangle_it1.60127938
X-RAY DIFFRACTIONr_scbond_it2.81633330
X-RAY DIFFRACTIONr_scangle_it4.1154.52866
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 166 -
Rwork0.213 2942 -
obs-3108 93.03 %
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)
12.67280.2772-0.13311.2523-0.07740.9502-0.0232-0.34890.05240.02150.0033-0.12480.06870.16990.01990.08140.038-0.03110.0740.01830.028719.6161-1.804914.4038
22.42690.0001-0.06670.60270.08571.5622-0.00350.30150.646-0.01330.0392-0.1-0.05870.1387-0.03570.073-0.0067-0.00090.05050.12980.21514.118414.4328-0.0647
32.3155-0.25590.04640.6707-0.32311.4239-0.04590.5445-0.1311-0.12790.0219-0.05750.21350.04530.02390.0687-0.0095-0.00090.0744-0.0211-0.002611.3306-7.1348-5.834
42.6872-0.3124-0.27050.9552-0.0070.6838-0.03930.33280.0593-0.05380.08930.13010.0963-0.2235-0.04990.0706-0.0296-0.04170.11240.09490.0423-19.2062-2.02343.2928
52.4241-0.0646-0.10330.7456-0.19211.354-0.013-0.25240.66540.08510.12560.0567-0.1033-0.1786-0.11260.0610.0731-0.01350.0461-0.02110.2174-13.619915.093616.7722
62.96570.26830.19691.0660.05131.122-0.0771-0.6669-0.12210.12360.08890.10820.1158-0.1098-0.01180.10160.04410.00820.16950.09470.0329-10.97-6.210523.8046
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 1675 - 167
22BB5 - 1675 - 167
33CC6 - 1676 - 167
44DD5 - 1675 - 167
55EE5 - 1675 - 167
66FF6 - 1676 - 167

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