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- PDB-4ouq: Crystal structure of a DUF4783 family protein (BF1468) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 4ouq
TitleCrystal structure of a DUF4783 family protein (BF1468) from Bacteroides fragilis YCH46 at 1.55 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DUF4783 / PF16022 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4783 / Domain of unknown function (DUF4783) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF4783 domain-containing protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BF1468) from Bacteroides fragilis YCH46 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,3561
Polymers12,3561
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.467, 48.316, 49.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 12355.815 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: YCH46 / Gene: BF1468 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q64WA7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 22-130) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 22-130) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.95 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 30.0% polyethylene glycol 6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→21.965 Å / Num. all: 13967 / Num. obs: 13967 / % possible obs: 96.4 % / Redundancy: 3.2 % / Rsym value: 0.064 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.55-1.5930.6451.6314210320.64597.7
1.59-1.632.90.5451.927829720.54594.1
1.63-1.683.40.4732.432659730.47398.1
1.68-1.733.30.3712.931539450.37198.5
1.73-1.793.20.33.529789290.397.9
1.79-1.853.10.2434.327388840.24396.6
1.85-1.922.90.185.324278330.1893.7
1.92-23.30.1347.326608100.13496.4
2-2.093.30.1079.327298160.10798.3
2.09-2.193.20.09410.524507570.09497.4
2.19-2.313.20.0811.823287250.0897.8
2.31-2.4530.07512.319766540.07592.4
2.45-2.623.30.0661421906550.06697.8
2.62-2.833.40.05416.521266180.05498.2
2.83-3.13.30.04418.318755660.04497.6
3.1-3.4730.0432115074960.04393
3.47-43.30.0423.114574480.0494.6
4-4.93.40.03925.512903810.03993.8
4.9-6.933.10.03121.18892900.03190
6.93-21.9653.30.02923.25961830.02993.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→21.965 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.483 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 691 5 %RANDOM
Rwork0.199 ---
obs0.2009 13930 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 90.68 Å2 / Biso mean: 26.1654 Å2 / Biso min: 10.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0 Å2-0 Å2
2--0.91 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.55→21.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 0 104 916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019887
X-RAY DIFFRACTIONr_bond_other_d0.0020.02862
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9251208
X-RAY DIFFRACTIONr_angle_other_deg0.75831966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.255120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48923.95848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10815158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.837159
X-RAY DIFFRACTIONr_chiral_restr0.110.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021069
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02238
X-RAY DIFFRACTIONr_mcbond_it2.8792.57439
X-RAY DIFFRACTIONr_mcbond_other2.8752.576440
X-RAY DIFFRACTIONr_mcangle_it3.5054.773551
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 61 -
Rwork0.282 962 -
all-1023 -
obs--97.24 %
Refinement TLS params.Method: refined / Origin x: 14.589 Å / Origin y: -1.2027 Å / Origin z: -4.6042 Å
111213212223313233
T0.0045 Å2-0.0091 Å20.0035 Å2-0.0295 Å20.0048 Å2--0.0319 Å2
L3.3882 °20.8542 °2-0.822 °2-2.01 °20.3411 °2--4.2668 °2
S-0.032 Å °0.0192 Å °0.0982 Å °-0.0672 Å °0.0358 Å °-0.1382 Å °-0.1034 Å °0.3395 Å °-0.0038 Å °

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