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- PDB-2oeq: Protein of Unknown Function (DUF964) from Bacillus stearothermophilus -

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Basic information

Entry
Database: PDB / ID: 2oeq
TitleProtein of Unknown Function (DUF964) from Bacillus stearothermophilus
ComponentsProtein of unknown function, DUF964
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / helix bundle / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyYheA/YmcA-like / Control of competence regulator ComK, YlbF/YmcA / YheA/YmcA-like domain superfamily / Control of competence regulator ComK, YlbF/YmcA / YheA-like fold / Up-down Bundle / Mainly Alpha / UPF0342 protein GK0640
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsKim, Y. / Wu, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Protein of Unknown Function from Bacillus stearothermophilus
Authors: Kim, Y. / Wu, R. / Collart, F. / Joachimiak, A.
History
DepositionDec 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT UNIPROT DATABASE AT THE TIME OF DEPOSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein of unknown function, DUF964
B: Protein of unknown function, DUF964
C: Protein of unknown function, DUF964
D: Protein of unknown function, DUF964


Theoretical massNumber of molelcules
Total (without water)58,1664
Polymers58,1664
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-98 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.901, 54.353, 59.629
Angle α, β, γ (deg.)69.67, 81.93, 72.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein of unknown function, DUF964


Mass: 14541.435 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5L2A5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.2M Potassium dihydrogen phosphate, 15% PEG3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907, 0.97923
DetectorType: SBC-2 / Detector: CCD / Date: Nov 2, 2003 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.979231
ReflectionResolution: 2.9→55.9 Å / Num. all: 10827 / Num. obs: 10827 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.25 % / Limit h max: 15 / Limit h min: -14 / Limit k max: 18 / Limit k min: -17 / Limit l max: 20 / Limit l min: 0 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1085 / % possible all: 70.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
SOLVEphasing
RESOLVEphasing
PHENIXphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→34.17 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.826 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.595 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31437 1110 10.3 %RANDOM
Rwork0.22222 ---
all0.23164 9717 --
obs0.23164 9717 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.145 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å2-0.69 Å20.52 Å2
2---0.07 Å2-1.67 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 0 88 3833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223789
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.975077
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2215456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.66824.258209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.1315764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6811544
X-RAY DIFFRACTIONr_chiral_restr0.1040.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022860
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3210.22316
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it16.1461.52307
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it22.05123681
X-RAY DIFFRACTIONr_scbond_it031482
X-RAY DIFFRACTIONr_scangle_it04.51396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.398 72
Rwork0.342 735
obs-807

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