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- PDB-1ylq: Crystal structure of putative nucleotidyltransferase -

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Basic information

Entry
Database: PDB / ID: 1ylq
TitleCrystal structure of putative nucleotidyltransferase
Componentsputative nucleotidyltransferase, hypothetical protein AF0614
KeywordsTRANSFERASE / nucleotidyltransferase / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyPolymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / nucleotidyltransferase activity / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta / Polymerase nucleotidyl transferase domain-containing protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.016 Å
AuthorsChang, C. / Joachimiak, A. / Skarina, T. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Hypothetical protein AF0614, putative nucleotidyltransferase
Authors: Chang, C. / Joachimiak, A. / Skarina, T. / Edwards, A. / Savchenko, A.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: putative nucleotidyltransferase, hypothetical protein AF0614
B: putative nucleotidyltransferase, hypothetical protein AF0614
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0614
Polymers22,8682
Non-polymers1922
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-36 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.350, 38.350, 244.082
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein putative nucleotidyltransferase, hypothetical protein AF0614


Mass: 11434.226 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O29641
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 5.5
Details: PEG3350, Ammonium Sulphate,B-Tris, pH 5.5, VAPOR DIFFUSION, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97775
SYNCHROTRONAPS 19-ID20.97774, 0.97970
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 24, 2004
ADSC QUANTUM 42CCDNov 24, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.977751
20.977741
30.97971
ReflectionResolution: 2→50 Å / Num. all: 15124 / Num. obs: 14806 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.016→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.883 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26746 744 5.1 %RANDOM
Rwork0.2166 ---
all0.21916 14755 --
obs0.2166 13974 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.016→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 10 126 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221604
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.9622140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9875184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88123.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29615324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6261512
X-RAY DIFFRACTIONr_chiral_restr0.1640.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021176
X-RAY DIFFRACTIONr_nbd_refined0.2360.2773
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.216
X-RAY DIFFRACTIONr_mcbond_it1.2211.5955
X-RAY DIFFRACTIONr_mcangle_it1.86521486
X-RAY DIFFRACTIONr_scbond_it3.0253750
X-RAY DIFFRACTIONr_scangle_it4.4684.5654
LS refinement shellResolution: 2.016→2.068 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 45 -
Rwork0.221 969 -
obs--99.22 %
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)
14.4636-1.37751.56254.0061-1.60685.6889-0.01170.2058-0.2956-0.0570.0148-0.0058-0.024-0.1681-0.0031-0.01560.01990.0251-0.08320.0075-0.0897-5.07611.724129.8362
23.1788-0.40162.44094.5524-2.55955.65410.0415-0.09910.11620.1348-0.01390.20270.2194-0.1294-0.0275-0.04330.0353-0.0151-0.0486-0.0152-0.0854-11.548222.982210.8335
32.86280.05580.75984.9964-1.53635.86870.00990.27250.0312-0.1315-0.1843-0.34530.01130.55290.1744-0.08820.0220.0276-0.09190.0304-0.03274.974611.389730.8115
43.5808-1.12550.55213.7452-1.59235.5348-0.1084-0.03190.3070.3349-0.0958-0.2338-0.40950.29060.2043-0.0770.0179-0.0324-0.1099-0.0025-0.0312-6.762331.8569.8482
59.0262-6.29970.86385.6704-1.09125.7579-0.1134-0.2884-0.26060.48840.09990.3928-0.0094-0.42850.01360.006-0.00710.0706-0.08610.0328-0.0574-10.5559.673339.6006
61.0284-2.20452.08710.899-1.11296.06560.1860.2963-0.119-0.478-0.13230.49190.4677-0.0945-0.0538-0.05940.0403-0.0606-0.0033-0.0515-0.0431-16.055919.22811.0914
71.4925-0.29212.43651.3427-4.053213.9263-0.1192-0.1475-0.1676-0.11840.09250.28980.242-0.51170.02670.04660.0631-0.0126-0.05230.0022-0.0314-12.588714.888320.308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 20
2X-RAY DIFFRACTION1A35 - 40
3X-RAY DIFFRACTION1A66 - 71
4X-RAY DIFFRACTION1A87 - 88
5X-RAY DIFFRACTION2B16 - 20
6X-RAY DIFFRACTION2B35 - 40
7X-RAY DIFFRACTION2B66 - 71
8X-RAY DIFFRACTION2B87 - 88
9X-RAY DIFFRACTION3A41 - 65
10X-RAY DIFFRACTION3A-1 - 15
11X-RAY DIFFRACTION4B41 - 65
12X-RAY DIFFRACTION4B-1 - 15
13X-RAY DIFFRACTION5A72 - 83
14X-RAY DIFFRACTION6B72 - 83
15X-RAY DIFFRACTION7A21 - 34
16X-RAY DIFFRACTION7B21 - 34

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