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- PDB-2wb7: pT26-6p -

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Basic information

Entry
Database: PDB / ID: 2wb7
TitlepT26-6p
ComponentsPT26-6P
KeywordsUNKNOWN FUNCTION / EXTRA CHROMOSOMAL ELEMENTS
Function / homologypT26-6p, five-helical bundle domain / Immunoglobulin-like - #2050 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Function and homology information
Biological speciesTHERMOCOCCUS SP. 26-2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKeller, J. / Leulliot, N. / Soler, N. / Collinet, B. / Vincentelli, R. / Forterre, P. / van Tilbeurgh, H.
CitationJournal: Protein Sci. / Year: 2009
Title: A Protein Encoded by a New Family of Mobile Elements from Euryarchaea Exhibits Three Domains with Novel Folds.
Authors: Keller, J. / Leulliot, N. / Soler, N. / Collinet, B. / Vincentelli, R. / Forterre, P. / Van Tilbeurgh, H.
History
DepositionFeb 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PT26-6P
B: PT26-6P


Theoretical massNumber of molelcules
Total (without water)118,5572
Polymers118,5572
Non-polymers00
Water4,053225
1
A: PT26-6P


Theoretical massNumber of molelcules
Total (without water)59,2791
Polymers59,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PT26-6P


Theoretical massNumber of molelcules
Total (without water)59,2791
Polymers59,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.150, 133.150, 164.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PT26-6P


Mass: 59278.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS SP. 26-2 (archaea) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.54 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growDetails: 1.5-2M (NH4)2SO4, 0.025M KH2PO4, 8% PEG 8000, 10 TO 16% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→47.19 Å / Num. obs: 50396 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 0.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
XDSdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→47.19 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.341 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2576 5.1 %RANDOM
Rwork0.193 ---
obs0.196 47748 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8274 0 0 225 8499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228462
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.94411510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1951048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06125.3400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7741528
X-RAY DIFFRACTIONr_chiral_restr0.0840.21280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216454
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.541.55222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06228420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51433240
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6614.53090
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 168 -
Rwork0.319 3254 -
obs--100 %

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