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- PDB-2rff: Crystal structure of a putative nucleotidyltransferase (NP_343093... -

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Basic information

Entry
Database: PDB / ID: 2rff
TitleCrystal structure of a putative nucleotidyltransferase (NP_343093.1) from Sulfolobus solfataricus at 1.40 A resolution
ComponentsPutative nucleotidyltransferase
KeywordsTRANSFERASE / NP_343093.1 / A Putative Nucleotidyltransferase / Nucleotidyltransferase domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


nucleotidyltransferase activity
Similarity search - Function
: / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polymerase nucleotidyl transferase domain-containing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative nucleotidyltransferase (NP_343093.1) from Sulfolobus solfataricus at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 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.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: 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
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2583
Polymers13,1331
Non-polymers1242
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.007, 29.884, 35.202
Angle α, β, γ (deg.)77.240, 73.720, 78.300
Int Tables number1
Space group name H-MP1
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative nucleotidyltransferase


Mass: 13133.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Species: Sulfolobus solfataricus / Strain: P2, DSM 1617, JCM 11322 / Gene: NP_343093.1, SSO1673 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97XP0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NANODROP, 20.0% PEG MME2000, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.4→33.278 Å / Num. obs: 16758 / % possible obs: 90.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Χ2: 1.274 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.4530.26110001.85854
1.45-1.513.20.22514431.62278
1.51-1.583.60.20317801.37194.3
1.58-1.663.80.17417611.30695.1
1.66-1.763.90.13417611.13896
1.76-1.93.90.10117661.10196.7
1.9-2.093.90.08117951.21296.7
2.09-2.393.90.06717991.28697.3
2.39-3.023.90.0618181.33398
3.02-33.2783.90.04618351.01799

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0040refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALEPACKdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
HKL-2000data reduction
SOLVEphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→33.278 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.929 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.073
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 851 5.1 %RANDOM
Rwork0.145 ---
obs0.147 16755 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.191 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20.68 Å2-0.2 Å2
2---0.48 Å2-2.13 Å2
3---3.09 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 8 107 1105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221026
X-RAY DIFFRACTIONr_bond_other_d0.0050.02757
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9871387
X-RAY DIFFRACTIONr_angle_other_deg1.42931852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8595140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.39523.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8815218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.724159
X-RAY DIFFRACTIONr_chiral_restr0.1080.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021149
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02223
X-RAY DIFFRACTIONr_nbd_refined0.2280.2172
X-RAY DIFFRACTIONr_nbd_other0.160.2792
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2484
X-RAY DIFFRACTIONr_nbtor_other0.0730.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.271
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.222
X-RAY DIFFRACTIONr_mcbond_it2.4592692
X-RAY DIFFRACTIONr_mcbond_other1.2182247
X-RAY DIFFRACTIONr_mcangle_it3.0564984
X-RAY DIFFRACTIONr_scbond_it3.5664472
X-RAY DIFFRACTIONr_scangle_it4.5086389
X-RAY DIFFRACTIONr_rigid_bond_restr1.59232069
X-RAY DIFFRACTIONr_sphericity_free6.7873107
X-RAY DIFFRACTIONr_sphericity_bonded4.29231755
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 31 -
Rwork0.214 674 -
all-705 -
obs--51.35 %

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