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- PDB-2nv4: Crystal structure of UPF0066 protein AF0241 in complex with S-ade... -

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Basic information

Entry
Database: PDB / ID: 2nv4
TitleCrystal structure of UPF0066 protein AF0241 in complex with S-adenosylmethionine. Northeast Structural Genomics Consortium target GR27
ComponentsUPF0066 protein AF_0241
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG GR27 Y241_ARCFU X-RAY / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


YaeB-like / Uncharacterised protein family UPF0066, conserved site / TsaA-like domain signature. / TrmO-like, N-terminal domain / YaeB-like superfamily / YaeB, N-terminal domain superfamily / YaeB-like / tRNA-methyltransferase O / TsaA-like domain profile. / Elongation Factor Tu (Ef-tu); domain 3 ...YaeB-like / Uncharacterised protein family UPF0066, conserved site / TsaA-like domain signature. / TrmO-like, N-terminal domain / YaeB-like superfamily / YaeB, N-terminal domain superfamily / YaeB-like / tRNA-methyltransferase O / TsaA-like domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / S-ADENOSYLMETHIONINE / S-adenosyl-L-methionine-binding protein AF_0241
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, J. / Vorobiev, S.M. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Vorobiev, S.M. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Struct.Funct.Genom. / Year: 2007
Title: Functional insights from structural genomics.
Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / ...Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / Pichersky, E. / Klessig, D.F. / Porter, C.W. / Montelione, G.T. / Tong, L.
History
DepositionNov 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: UPF0066 protein AF_0241
B: UPF0066 protein AF_0241
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8485
Polymers33,9922
Non-polymers8563
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-26 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.812, 73.496, 78.545
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 UPF0066 protein AF_0241


Mass: 16996.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0241 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O29998
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Na-Acetate, 18% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 27026 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.55 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 315832.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1154 4.9 %RANDOM
Rwork0.201 ---
obs0.201 23641 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8179 Å2 / ksol: 0.380621 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.3 Å20 Å20 Å2
2--3.35 Å20 Å2
3----6.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 58 52 2242
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4acy.paracy.top
X-RAY DIFFRACTION5sam.parsam.top

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