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- PDB-1y82: Conserved hypothetical protein Pfu-367848-001 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 1y82
TitleConserved hypothetical protein Pfu-367848-001 from Pyrococcus furiosus
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / SECSG / PSI / Southeast Collaboratory for Structural Genomics / Protein Structure Initiative / Pyrococcus furiosus / Pfu-367848-001 / hyperthermophile
Function / homology
Function and homology information


RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Probable ribonuclease VapC, Thermococci / PIN domain / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
VapC ribonuclease PF0355
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 2.3 Å
AuthorsHoranyi, P. / Tempel, W. / Habel, J. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Florence, Q. / Zhou, W. / Lin, D. ...Horanyi, P. / Tempel, W. / Habel, J. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Liu, Z.-J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Conserved hypothetical protein Pfu-367848-001 from Pyrococcus furiosus
Authors: Horanyi, P. / Tempel, W. / Habel, J. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / ...Authors: Horanyi, P. / Tempel, W. / Habel, J. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Liu, Z.-J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
History
DepositionDec 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / 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 / _pdbx_database_related.db_name / _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
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 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
C: hypothetical protein
D: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)73,85046
Polymers73,8504
Non-polymers042
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: hypothetical protein
D: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)36,92524
Polymers36,9252
Non-polymers022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-29 kcal/mol
Surface area13460 Å2
MethodPISA, PQS
3
A: hypothetical protein
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)36,92522
Polymers36,9252
Non-polymers020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-29 kcal/mol
Surface area13850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.601, 103.667, 104.253
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
hypothetical protein /


Mass: 18462.424 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U3V0
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 42 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 291 K / Method: modified microbatch / pH: 5.5
Details: 0.1M citrate, 0.1M sodium chloride, 0.1M lithium sulfate, 30% v/v PEG 400, pH 5.5, modified microbatch, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97623
SYNCHROTRONAPS 22-BM20.97623
Detector
TypeIDDetector
MARMOSAIC 225 mm CCD1CCD
mar1652CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 28211 / % possible obs: 98.7 % / Rmerge(I) obs: 0.109 / Χ2: 2.127
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2Diffraction-ID% possible all
2.3-2.380.34927880.8831,299.7
2.38-2.480.26528111.0011,299.8
2.48-2.590.19928191.0421,299.9
2.59-2.730.15528111.2251,2100
2.73-2.90.13928251.2971,2100
2.9-3.120.1128261.6531,2100
3.12-3.440.10228492.371,2100
3.44-3.930.09625113.4711,287.6
3.93-4.950.07629183.551,2100
4.95-400.07230535.0561,299.9

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Phasing

PhasingMethod: sad
Phasing MADD res high: 2.4 Å / D res low: 20 Å / FOM : 0.39 / Reflection: 23668
Phasing MAD shell
Resolution (Å)FOM Reflection
8.22-200.361303
5.33-8.220.442067
4.21-5.330.452601
3.59-4.210.452995
3.18-3.590.453329
2.88-3.180.43626
2.66-2.880.343821
2.48-2.660.293926
Phasing dmFOM : 0.62 / FOM acentric: 0.64 / FOM centric: 0.5 / Reflection: 23668 / Reflection acentric: 20942 / Reflection centric: 2726
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.9-19.4040.850.850.691105787318
4.3-6.90.790.820.6333272772555
3.4-4.30.80.820.6341043583521
3-3.40.690.710.540533629424
2.6-30.520.540.3469736364609
2.4-2.60.370.380.241063807299

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
ARP/wARPmodel building
RefinementMethod to determine structure: SAS / Resolution: 2.3→73.521 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.211 / SU R Cruickshank DPI: 0.367 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.265 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 875 3.111 %THIN SHELLS
Rwork0.2216 ---
all0.223 ---
obs0.22346 28124 98.353 %-
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: 21.477 Å2
Baniso -1Baniso -2Baniso -3
1-1.792 Å20 Å20 Å2
2---1.609 Å20 Å2
3----0.183 Å2
Refinement stepCycle: LAST / Resolution: 2.3→73.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 42 39 4554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224537
X-RAY DIFFRACTIONr_angle_refined_deg1.3812.0086153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40625.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82715851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4581515
X-RAY DIFFRACTIONr_chiral_restr0.090.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023179
X-RAY DIFFRACTIONr_nbd_refined0.2010.22098
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.28
X-RAY DIFFRACTIONr_mcbond_it2.65522901
X-RAY DIFFRACTIONr_mcangle_it4.08934728
X-RAY DIFFRACTIONr_scbond_it3.43421636
X-RAY DIFFRACTIONr_scangle_it4.90131425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.3560.323700.2221940207696.821
2.356-2.420.321700.221958203599.656
2.42-2.490.289350.2211934197099.949
2.49-2.5670.33700.2371817188999.894
2.567-2.6510.307700.23418031873100
2.651-2.7440.343350.23317781813100
2.744-2.8470.34700.23916551725100
2.847-2.9630.247350.2416541689100
2.963-3.0950.245700.24415431613100
3.095-3.2460.281350.22815181553100
3.246-3.4210.301350.22514431478100
3.421-3.6280.29350.2041000138974.514
3.628-3.8780.287700.1971240133598.127
3.878-4.1870.202350.1921177121899.507
4.187-4.5860.256350.17911161151100
4.586-5.1240.178350.1949941029100
5.124-5.91200.241935935100
5.912-7.2290.353350.284767802100
7.229-10.1750.247350.19759262899.841
10.175-73.52100.30438539497.716

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