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- PDB-2pk8: Crystal structure of an uncharacterized protein PF0899 from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 2pk8
TitleCrystal structure of an uncharacterized protein PF0899 from Pyrococcus furiosus
ComponentsUncharacterized protein PF0899
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF0899 / PYROCOCCUS FURIOSUS / UNCHARACTERIZED PROTEIN / PSI / PROTEIN STRUCTURE INITIATIVE / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG
Function / homologyPutative type 4B encapsulin shell protein / Putative type 4B encapsulin shell protein superfamily / Putative type 4B encapsulin shell protein / hypothetical protein PF0899 domain / hypothetical protein PF0899 fold / 2-Layer Sandwich / Alpha Beta / GOLD (I) CYANIDE ION / DUF1884 domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.85 Å
AuthorsLiu, Z.J. / Tempel, W. / Chen, L. / Shah, A. / Lee, D. / Clancy-Kelley, L.L. / Dillard, B.D. / Rose, J.P. / Sugar, F.J. / Jenny Jr., F.E. ...Liu, Z.J. / Tempel, W. / Chen, L. / Shah, A. / Lee, D. / Clancy-Kelley, L.L. / Dillard, B.D. / Rose, J.P. / Sugar, F.J. / Jenny Jr., F.E. / Lee, H.S. / Izumi, M. / Shah, C. / Poole III, F.L. / Adams, M.W.W. / Richardson, J.S. / Richardson, D.C. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution.
Authors: Kelley, L.L. / Dillard, B.D. / Tempel, W. / Chen, L. / Shaw, N. / Lee, D. / Newton, M.G. / Sugar, F.J. / Jenney, F.E. / Lee, H.S. / Shah, C. / Poole, F.L. / Adams, M.W. / Richardson, J.S. / ...Authors: Kelley, L.L. / Dillard, B.D. / Tempel, W. / Chen, L. / Shaw, N. / Lee, D. / Newton, M.G. / Sugar, F.J. / Jenney, F.E. / Lee, H.S. / Shah, C. / Poole, F.L. / Adams, M.W. / Richardson, J.S. / Richardson, D.C. / Liu, Z.J. / Wang, B.C. / Rose, J.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionMay 22, 2007ID: 1SHE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein PF0899
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8192
Polymers11,5701
Non-polymers2491
Water68538
1
A: Uncharacterized protein PF0899
hetero molecules

A: Uncharacterized protein PF0899
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6394
Polymers23,1412
Non-polymers4982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)47.080, 47.080, 83.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-500-

AUC

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Components

#1: Protein Uncharacterized protein PF0899


Mass: 11570.343 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M.W.W.ADAMS, P.S.BRERETON, M.IZUMI, F.E.JENNEY JR., H-S.LEE, F.L.POOLE II, C.SHAH, F.SUGAR) ...Details: THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M.W.W.ADAMS, P.S.BRERETON, M.IZUMI, F.E.JENNEY JR., H-S.LEE, F.L.POOLE II, C.SHAH, F.SUGAR) UNDER THE DIRECTION OF M.W.W.ADAMS.
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Species: Pyrococcus furiosus / Strain: DSM 3638, JCM 8422, Vc1 / Gene: PF0899 / Plasmid: pET24D BAM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR DE3 PRIL / References: UniProt: Q8U2E0
#2: Chemical ChemComp-AUC / GOLD (I) CYANIDE ION


Mass: 249.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2AuN2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.9
Details: MODIFIED MICROBATCH USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10 mg/mL) AND A PRECIPITANT SOLUTION CONTAINING 8% PEG 4000 IN 100mM SODIUM ACETATE, pH 3.9, ...Details: MODIFIED MICROBATCH USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10 mg/mL) AND A PRECIPITANT SOLUTION CONTAINING 8% PEG 4000 IN 100mM SODIUM ACETATE, pH 3.9, TEMPERATURE 291K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2003 / Details: Rosenbaum
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 9476 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Rsym value: 0.044
Reflection shellResolution: 1.85→1.92 Å / Rsym value: 0.251 / % possible all: 92.4

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
SERGUIdata collection
MAR345data collection
SCALEPACKdata scaling
SCA2structurephasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.85→19.81 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.053 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.257 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24249 443 4.7 %RANDOM
Rwork0.20662 ---
all0.2083 8896 --
obs0.2083 8896 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.48 Å20 Å2
2--0.97 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 3 38 765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022753
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7232.0081008
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.58125.75833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40615155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.62154
X-RAY DIFFRACTIONr_chiral_restr0.1130.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2336
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2521
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.011.5493
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4892754
X-RAY DIFFRACTIONr_scbond_it2.5953300
X-RAY DIFFRACTIONr_scangle_it3.8954.5254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 26 -
Rwork0.347 555 -
obs--86.33 %
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)
14.04691.1847-3.71379.322-10.216118.8312-0.0131-0.3820.15250.22050.124-0.4985-0.7070.4165-0.11090.1183-0.0050.04430.121-0.09790.10754.84522.84415.986
23.25940.9994-3.24050.5362-1.44924.12520.11020.42220.15980.1906-0.12240.2443-0.2566-0.28550.01220.09730.02840.02780.0922-0.00530.03273.66920.7754.635
310.49883.9073-9.40143.0659-4.410912.6535-0.5-0.2747-0.37080.23890.01330.16530.75170.06630.48670.27320.04240.08440.02990.01390.14232.1317.34917.193
427.1427-0.041853.007645.1013-61.8158188.021-3.18210.22830.58241.65091.83794.58224.83291.92131.34420.6612-0.2821-0.02090.2071-0.1170.4062-7.3685.14716.439
55.2904-0.7685-2.75592.0575-1.06595.2956-0.08990.2433-0.3616-0.0666-0.1090.17110.4419-0.40720.19890.1477-0.0270.04370.0826-0.0350.10472.00212.37.466
60.80220.9782-1.69764.4026-3.14917.4803-0.0051-0.12920.06880.2263-0.1975-0.0985-0.3340.16490.20260.04730.00590.01680.07190.00680.06059.70320.9214.657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2510 - 33
2X-RAY DIFFRACTION2AA26 - 3334 - 41
3X-RAY DIFFRACTION3AA34 - 5042 - 58
4X-RAY DIFFRACTION4AA51 - 5359 - 61
5X-RAY DIFFRACTION5AA54 - 7062 - 78
6X-RAY DIFFRACTION6AA71 - 9479 - 102

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