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- PDB-3d7a: Crystal structure of DUF54 family protein PH1010 from hyperthermo... -

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Basic information

Entry
Database: PDB / ID: 3d7a
TitleCrystal structure of DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3
ComponentsUPF0201 protein PH1010
KeywordsUNKNOWN FUNCTION / DUF54 family
Function / homologyUncharacterised protein family UPF0201 / RNA binding / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / 2-Layer Sandwich / Alpha Beta / UPF0201 protein PH1010
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsShirokane, M. / Miyazono, K.I. / Sawano, Y. / Tanokura, M.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3.
Authors: Miyazono, K.I. / Shirokane, M. / Sawano, Y. / Tanokura, M.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Mar 20, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: UPF0201 protein PH1010
B: UPF0201 protein PH1010


Theoretical massNumber of molelcules
Total (without water)32,1562
Polymers32,1562
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-7 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.934, 49.526, 132.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UPF0201 protein PH1010 / DUF54 family protein


Mass: 16077.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1010 / Production host: Escherichia coli (E. coli) / References: UniProt: O58738
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.4 Å3/Da / Density % sol: 48.75 % / Mosaicity: 0.259 °

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 25090 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.061 / Χ2: 2.068 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.976.60.2924541.01899.8
1.97-2.056.80.22124681.14599.8
2.05-2.146.90.16524681.33599.8
2.14-2.256.90.12724741.551100
2.25-2.3970.10824771.812100
2.39-2.5870.08925032.04100
2.58-2.8470.07525142.31599.9
2.84-3.2570.06825362.95100
3.25-4.096.80.05925493.73699.8
4.09-306.50.04426472.6497.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.498 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28083 1279 5.1 %RANDOM
Rwork0.23775 ---
obs0.23987 23779 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 0 176 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222258
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9913041
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2995269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81224.231104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41815442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8871516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211672
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_it0.8911.51351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59722199
X-RAY DIFFRACTIONr_scbond_it2.5093907
X-RAY DIFFRACTIONr_scangle_it4.1664.5842
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 101 -
Rwork0.268 1691 -
all-1793 -
obs--99.45 %

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