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- PDB-1xg7: Conserved hypothetical protein Pfu-877259-001 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 1xg7
TitleConserved hypothetical protein Pfu-877259-001 from Pyrococcus furiosus
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / Southeast Collaboratory for Structural Genomics / SECSG / hyperthermophile / Pyrococcus furiosus / protein structure initiative / PSI
Function / homology
Function and homology information


oxidized base lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair
Similarity search - Function
N-glycosylase/DNA lyase-like / N-glycosylase/DNA lyase / N-glycosylase/DNA lyase / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / Endonuclease III; domain 1 / DNA glycosylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsChang, J. / Zhao, M. / Horanyi, P. / Xu, H. / Yang, H. / Liu, Z.-J. / Chen, L. / Zhou, W. / Habel, J. / Tempel, W. ...Chang, J. / Zhao, M. / Horanyi, P. / Xu, H. / Yang, H. / Liu, Z.-J. / Chen, L. / Zhou, W. / Habel, J. / Tempel, W. / Lee, D. / Lin, D. / Chang, S.-H. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr., F.E. / Lee, H.-S. / Li, T. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Chen, C.-Y. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Adams, M.W.W. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Conserved hypothetical protein Pfu-877259-001 from Pyrococcus furiosus
Authors: Chang, J. / Zhao, M. / Horanyi, P. / Xu, H. / Yang, H. / Liu, Z.-J. / Chen, L. / Zhou, W. / Habel, J. / Tempel, W. / Lee, D. / Lin, D. / Chang, S.-H. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr. ...Authors: Chang, J. / Zhao, M. / Horanyi, P. / Xu, H. / Yang, H. / Liu, Z.-J. / Chen, L. / Zhou, W. / Habel, J. / Tempel, W. / Lee, D. / Lin, D. / Chang, S.-H. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr., F.E. / Lee, H.-S. / Li, T. / Poole II, F.L. / Shah, C. / Sugar, F.J. / CHEN, C.-Y. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / ADAMS, M.W.W. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionSep 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 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 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)58,5962
Polymers58,5962
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.688, 81.639, 90.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYTRPTRPAA10 - 13018 - 138
2GLYGLYTRPTRPBB10 - 13018 - 138
3VALVALLYSLYSAA150 - 180158 - 188
4VALVALLYSLYSBB150 - 180158 - 188
5GLNGLNLEULEUAA200 - 240208 - 248
6GLNGLNLEULEUBB200 - 240208 - 248

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Components

#1: Protein hypothetical protein


Mass: 29298.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U2D5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 291 K
Details: 25w/v% PEG 3350, 0.15M potassium nitrate, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9785
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 40388 / % possible obs: 98.1 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 1.88→1.95 Å / Rmerge(I) obs: 0.159 / % possible all: 93.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→37.22 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / ESU R Free: 0.165 / Stereochemistry target values: ENGH & HUBER / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2025 5.027 %THIN SHELLS
Rwork0.207 ---
obs0.21 40282 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.098 Å20 Å20 Å2
2--0.048 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.88→37.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 0 133 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223972
X-RAY DIFFRACTIONr_bond_other_d00.023723
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.975369
X-RAY DIFFRACTIONr_angle_other_deg3.65638604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5823.21162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52715707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7051524
X-RAY DIFFRACTIONr_chiral_restr0.0820.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024311
X-RAY DIFFRACTIONr_gen_planes_other0.010.02828
X-RAY DIFFRACTIONr_nbd_refined0.2110.2903
X-RAY DIFFRACTIONr_nbd_other0.2140.23220
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21974
X-RAY DIFFRACTIONr_nbtor_other0.1060.21700
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3620.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.2681.52411
X-RAY DIFFRACTIONr_mcbond_other01.5981
X-RAY DIFFRACTIONr_mcangle_it3.32923885
X-RAY DIFFRACTIONr_scbond_it2.47131561
X-RAY DIFFRACTIONr_scangle_it3.7354.51484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3014 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.520.5
medium thermal1.62
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 135 -
Rwork0.303 2440 -
obs--85.86 %

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