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- PDB-1xi6: Extragenic suppressor from Pyrococcus furiosus Pfu-1862794-001 -

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Basic information

Entry
Database: PDB / ID: 1xi6
TitleExtragenic suppressor from Pyrococcus furiosus Pfu-1862794-001
Componentsextragenic suppressor
KeywordsStructural genomics / unknown function / Pyrococcus furiosus / extragenic suppressor / Southeast Collaboratory for Structural Genomics / hyperthermophile / PSI / Protein Structure Initiative / SECSG
Function / homology
Function and homology information


: / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / metal ion binding
Similarity search - Function
Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fructose-1,6-bisphosphatase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsZhao, M. / Chang, J.C. / Zhou, W. / Chen, L. / Horanyi, P. / Xu, H. / Yang, H. / Liu, Z.-J. / Habel, J.E. / Lee, D. ...Zhao, M. / Chang, J.C. / Zhou, W. / Chen, L. / Horanyi, P. / Xu, H. / Yang, H. / Liu, Z.-J. / Habel, J.E. / Lee, D. / Chang, S.-H. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Extragenic suppressor from Pyrococcus furiosus Pfu-1862794-001
Authors: Zhao, M. / Chang, J.C. / Zhou, W. / Chen, L. / Horanyi, P. / Xu, H. / Yang, H. / Liu, Z.-J. / Habel, J.E. / Lee, D. / Chang, S.-H. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionSep 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 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 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: extragenic suppressor


Theoretical massNumber of molelcules
Total (without water)28,8751
Polymers28,8751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.613, 81.613, 293.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein extragenic suppressor


Mass: 28875.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET24d Bam / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star DE3 pRIL / References: UniProt: Q8TZH9

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.97 %
Crystal growTemperature: 291 K / Method: modified microbatch / pH: 6.2
Details: 0.3-0.9M ammonium dihydrogen phosphate, 30%v/v glycerol, 0.07M MES, pH 6.2, modified microbatch, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16734 / % possible obs: 83.4 % / Rmerge(I) obs: 0.136 / Χ2: 1.545
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
2.4-2.490.2546400.59433.1
2.49-2.590.34210510.77153.4
2.59-2.70.35513371.01168.4
2.7-2.850.30416101.02481.4
2.85-3.020.34418620.99193.5
3.02-3.260.34519951.02899.9
3.26-3.580.24619941.375100
3.58-4.10.16220121.79100
4.1-5.170.11520532.054100
5.17-500.09321801.92599.5

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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
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DK4
Resolution: 2.8→26.86 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.871 / SU B: 13.979 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29828 612 4.9 %RANDOM
Rwork0.27094 ---
obs0.27224 11906 98.26 %-
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: 46.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 0 0 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221722
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9742343
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3185231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13724.37564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60915253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.642158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021281
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.2755
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21205
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0840.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it01.51179
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it021836
X-RAY DIFFRACTIONr_scbond_it03609
X-RAY DIFFRACTIONr_scangle_it04.5507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
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 (%)
2.801-2.8730.329400.43674590686.55
2.873-2.950.364420.36776988192.054
2.95-3.0350.405510.34979887696.918
3.035-3.1270.469260.337796822100
3.127-3.2280.325420.322784826100
3.228-3.340.406410.314749790100
3.34-3.4640.272420.303719761100
3.464-3.6030.249320.275720752100
3.603-3.760.315300.276685715100
3.76-3.9390.312400.24464368499.854
3.939-4.1470.25300.24962665799.848
4.147-4.3920.263310.236587618100
4.392-4.6870.35300.238557587100
4.687-5.0490.299260.225531557100
5.049-5.5120.238320.239482514100
5.512-6.130.267190.28457476100
6.13-7.0180.327250.289397422100
7.018-8.4520.249120.239361373100
8.452-11.4020.205130.188296309100
11.402-26.8610.23780.34320621599.535

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