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- PDB-4pgo: Crystal structure of hypothetical protein PF0907 from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 4pgo
TitleCrystal structure of hypothetical protein PF0907 from Pyrococcus furiosus solved by sulfur SAD using Swiss Light Source data
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Sulfur SAD / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / STRUCTURAL GENOMICS
Function / homologyUncharacterised conserved protein UCP019072 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Translation protein, beta-barrel domain superfamily / Beta Barrel / Mainly Beta / Elongation factor Tu-type domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWeinert, T. / Waltersperger, S. / Olieric, V. / Panepucci, E. / Chen, L. / Rose, J.P. / Wang, M. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination.
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7753
Polymers12,7041
Non-polymers712
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.500, 88.500, 73.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein / HYPOTHETICAL PROTEIN PF0907


Mass: 12703.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0907 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U2D2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: MODIFIED MICROBATCH UNDER OIL USING 1.6M MAGNESIUM SULFATE IN 0.1M MES BUFFER, PH 6.5, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.066 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13544 / Num. obs: 7558 / % possible obs: 94.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 51.16 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 69.96

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXDEphasing
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
SHELXmodel building
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.25 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 20.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2026 1330 9.82 %
Rwork0.1875 --
obs0.189 7558 94.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms635 0 2 6 643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009639
X-RAY DIFFRACTIONf_angle_d1.076858
X-RAY DIFFRACTIONf_dihedral_angle_d10.862235
X-RAY DIFFRACTIONf_chiral_restr0.038104
X-RAY DIFFRACTIONf_plane_restr0.004110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39180.28111260.24341157X-RAY DIFFRACTION80
2.3918-2.50070.21441430.22021282X-RAY DIFFRACTION91
2.5007-2.63250.27011470.20941314X-RAY DIFFRACTION92
2.6325-2.79740.24741440.21141365X-RAY DIFFRACTION96
2.7974-3.01330.22961530.19241391X-RAY DIFFRACTION98
3.0133-3.31650.23271490.1821430X-RAY DIFFRACTION99
3.3165-3.79620.19931500.17531415X-RAY DIFFRACTION99
3.7962-4.78190.17071560.16381427X-RAY DIFFRACTION100
4.7819-44.25820.1951620.20161432X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0132-0.0685-0.03970.28620.19180.1178-0.213-0.1137-0.10930.00240.1551-0.22740.01170.1903-0.00010.5356-0.0455-0.02590.7206-0.01510.498375.24220.69312.4499
20.3788-0.40980.18480.4132-0.1970.07950.09180.39-0.00570.08540.6441-0.57340.6263-0.17620.0010.6234-0.0097-0.01870.59510.07690.629658.265925.9657-7.0307
30.9394-0.6255-0.85310.44160.51030.78490.28360.12410.1508-0.47910.299-0.61140.28970.522700.5518-0.063-0.02470.55230.01970.514265.300723.13163.2345
40.8408-0.29360.83340.49450.2781.531-0.29730.47220.6131-0.43940.30220.319-0.3195-0.19930.00110.6573-0.1557-0.10570.5065-0.00650.590267.495728.69191.8138
50.99621.0894-0.14521.2051-0.04120.2673-0.23380.06020.0454-0.25180.1265-0.2037-0.21760.3966-0.00020.569-0.0603-0.03390.5738-0.08710.574867.581223.06041.4237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 77 )
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 108 )

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