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- PDB-4fr9: Crystal structure of a BLIP-like protein (BF1215) from Bacteroide... -

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Basic information

Entry
Database: PDB / ID: 4fr9
TitleCrystal structure of a BLIP-like protein (BF1215) from Bacteroides fragilis NCTC 9343 at 1.20 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / BLIP-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyNuclear Transport Factor 2; Chain: A, - #360 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BF1215) from Bacteroides fragilis NCTC 9343 at 1.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)16,4981
Polymers16,4981
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.879, 36.977, 115.061
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: 16497.873 Da / Num. of mol.: 1 / Fragment: UNP residues 24-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF1215, BF9343_1154 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LG06, UniProt: A0A0K6BSL6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT (RESIDUES 24-166) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...1. THE CONSTRUCT (RESIDUES 24-166) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.00M ammonium sulfate, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97919
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.2→115.061 Å / Num. all: 48774 / Num. obs: 48774 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 17.008 Å2 / Rsym value: 0.046 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.2-1.2340.7251.41386634840.72599.1
1.23-1.264.70.5261.41618434490.52699.8
1.26-1.34.70.3831.91587433760.38399.8
1.3-1.344.70.3022.41537632670.30299.9
1.34-1.394.70.242.71524032190.24100
1.39-1.434.70.1943.81467530920.194100
1.43-1.494.80.14451406229520.144100
1.49-1.554.80.1086.51376728790.108100
1.55-1.624.80.0788.81326527730.078100
1.62-1.74.80.06710.31263926340.067100
1.7-1.794.80.05811.11216825380.058100
1.79-1.94.80.05311.51146923820.053100
1.9-2.034.80.0511.71085122540.05100
2.03-2.194.80.0414.11017021080.04100
2.19-2.45.50.04113.81082419590.041100
2.4-2.687.70.04912.31378617830.049100
2.68-3.18.30.04712.91309515870.047100
3.1-3.797.40.04414.2993213440.04499.5
3.79-5.375.90.03416.8627610690.03499.1
5.37-115.0615.40.03318.933876250.03395.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHARPphasing
SHELXphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→115.061 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.2 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.036
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2.THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION AND LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY). 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1717 2461 5.1 %RANDOM
Rwork0.1458 ---
obs0.147 48663 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.12 Å2 / Biso mean: 25.6264 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.2→115.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 0 188 1302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221240
X-RAY DIFFRACTIONr_bond_other_d0.0010.02772
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9481728
X-RAY DIFFRACTIONr_angle_other_deg0.9531921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68626.56767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16715.105191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.08152
X-RAY DIFFRACTIONr_chiral_restr0.0990.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02233
X-RAY DIFFRACTIONr_mcbond_it2.73751
X-RAY DIFFRACTIONr_mcbond_other2.253296
X-RAY DIFFRACTIONr_mcangle_it3.98651235
X-RAY DIFFRACTIONr_scbond_it4.6098489
X-RAY DIFFRACTIONr_scangle_it6.63311478
X-RAY DIFFRACTIONr_rigid_bond_restr2.04532012
X-RAY DIFFRACTIONr_sphericity_free9.2263198
X-RAY DIFFRACTIONr_sphericity_bonded5.98731965
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 180 -
Rwork0.328 3292 -
all-3472 -
obs--98.69 %

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