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- PDB-1xx7: Conserved hypothetical protein from Pyrococcus furiosus Pfu-403030-001 -

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Basic information

Entry
Database: PDB / ID: 1xx7
TitleConserved hypothetical protein from Pyrococcus furiosus Pfu-403030-001
Componentsoxetanocin-like protein
Keywordsstructural genomics / unknown function / PSI / SECSG / protein structure initiative / southeast collaboratory for structural genomics / Pyrococcus furiosus / conserved hypothetical protein / hyperthermophile
Function / homology
Function and homology information


5'-deoxynucleotidase / 5'-deoxynucleotidase activity
Similarity search - Function
HD domain / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / 5'-deoxynucleotidase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 2.261 Å
AuthorsChen, L. / Tempel, W. / Habel, J. / Zhou, W. / Nguyen, D. / Chang, S.-H. / Lee, D. / Kelley, L.-L.C. / Dillard, B.D. / Liu, Z.-J. ...Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Nguyen, D. / Chang, S.-H. / Lee, D. / Kelley, L.-L.C. / Dillard, B.D. / Liu, Z.-J. / Bridger, S. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr, F.E. / Lee, H.-S. / Li, T. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Conserved hypothetical protein from Pyrococcus furiosus Pfu-403030-001
Authors: Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Nguyen, D. / Chang, S.-H. / Lee, D. / Kelley, L.-L.C. / Dillard, B.D. / Liu, Z.-J. / Bridger, S. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr, F.E. ...Authors: Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Nguyen, D. / Chang, S.-H. / Lee, D. / Kelley, L.-L.C. / Dillard, B.D. / Liu, Z.-J. / Bridger, S. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr, F.E. / Lee, H.-S. / Li, T. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionNov 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 6 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 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: oxetanocin-like protein
B: oxetanocin-like protein
C: oxetanocin-like protein
D: oxetanocin-like protein
E: oxetanocin-like protein
F: oxetanocin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,06231
Polymers126,7106
Non-polymers35225
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19950 Å2
ΔGint-223 kcal/mol
Surface area35370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.073, 111.335, 125.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsnot known

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Components

#1: Protein
oxetanocin-like protein


Mass: 21118.373 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U3R1
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% v/v PEG 2000 MME, 0.2M ammonium sulfate, 0.1M ammonium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.969 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 64843 / % possible obs: 99.9 % / Rmerge(I) obs: 0.061 / Χ2: 0.953
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
2.25-2.330.35863750.93799.4
2.33-2.420.25463920.848100
2.42-2.530.19563780.804100
2.53-2.670.1564590.89100
2.67-2.830.1164350.816100
2.83-3.050.08564490.852100
3.05-3.360.05964820.922100
3.36-3.850.04564871.099100
3.85-4.840.03465881.274100
4.84-300.02667981.073100

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Phasing

PhasingMethod: sad
Phasing MADD res high: 3.8 Å / D res low: 20 Å / FOM : 0.24 / Reflection: 13845
Phasing MAD shell
Resolution (Å)FOM Reflection
11.84-200.25844
8.11-11.840.271213
6.53-8.110.311486
5.61-6.530.271691
4.99-5.610.251918
4.54-4.990.222083
4.2-4.540.222249
3.92-4.20.22361
Phasing dmFOM : 0.6 / FOM acentric: 0.6 / FOM centric: 0.55 / Reflection: 22915 / Reflection acentric: 20341 / Reflection centric: 2574
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.1-19.9570.850.850.69981715266
5.7-9.10.70.720.5931472635512
4.6-5.70.70.710.5839003423477
4-4.60.710.720.5938903491399
3.4-40.550.550.568076212595
3.2-3.40.360.360.3641903865325

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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
MolProbitymodel building
RefinementMethod to determine structure: SAD / Resolution: 2.261→83.333 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.19 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.199 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 2015 3.111 %thin shells
Rwork0.1995 ---
all0.201 ---
obs0.20098 64776 99.415 %-
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: 30.862 Å2
Baniso -1Baniso -2Baniso -3
1-0.148 Å20 Å20 Å2
2---0.367 Å20 Å2
3---0.218 Å2
Refinement stepCycle: LAST / Resolution: 2.261→83.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7728 0 25 69 7822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227840
X-RAY DIFFRACTIONr_bond_other_d00.027614
X-RAY DIFFRACTIONr_angle_refined_deg1.4612.00310631
X-RAY DIFFRACTIONr_angle_other_deg3.718317539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55325.118297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.472151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7921532
X-RAY DIFFRACTIONr_chiral_restr0.0830.21292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028545
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021425
X-RAY DIFFRACTIONr_nbd_refined0.2080.21861
X-RAY DIFFRACTIONr_nbd_other0.2190.26558
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23915
X-RAY DIFFRACTIONr_nbtor_other0.1050.23514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.25
X-RAY DIFFRACTIONr_mcbond_it2.55425015
X-RAY DIFFRACTIONr_mcbond_other022040
X-RAY DIFFRACTIONr_mcangle_it3.8338024
X-RAY DIFFRACTIONr_mcangle_other2.4936925
X-RAY DIFFRACTIONr_scbond_it2.78222825
X-RAY DIFFRACTIONr_scbond_other025574
X-RAY DIFFRACTIONr_scangle_it4.07632607
X-RAY DIFFRACTIONr_scangle_other2.178310614
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 (%)
2.261-2.3190.3451240.2484292475292.929
2.319-2.3830.2491550.2134451461299.87
2.383-2.4520.2651550.2143644519100
2.452-2.5270.2371240.20342704394100
2.527-2.610.2761240.20341074231100
2.61-2.7010.2781240.20340164140100
2.701-2.8030.2491240.20738784002100
2.803-2.9180.2641240.21936903814100
2.918-3.0470.2751240.21935723696100
3.047-3.1960.271930.20534313524100
3.196-3.3680.2651240.20732523376100
3.368-3.5720.277930.19830713164100
3.572-3.8180.233930.18629273020100
3.818-4.1240.195930.17427202813100
4.124-4.5160.21620.15725182580100
4.516-5.0470.197930.16822612354100
5.047-5.8250.237620.20320442106100
5.825-7.1250.267620.23717311793100
7.125-10.040.189310.17913901421100
10.04-83.3330.256310.26377684695.39

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