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- PDB-3sbu: Crystal structure of a ntf2-like protein (BF2862) from Bacteroide... -

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Basic information

Entry
Database: PDB / ID: 3sbu
TitleCrystal structure of a ntf2-like protein (BF2862) from Bacteroides fragilis NCTC 9343 at 2.15 A resolution
ComponentsHypothetical ntf2-like protein
KeywordsStructural Genomics / Unknown function / Cystatin-like / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4348 / Domain of unknown function (DUF4348) / Prokaryotic membrane lipoprotein lipid attachment site profile. / DI(HYDROXYETHYL)ETHER / DUF4348 domain-containing protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical ntf2-like protein (BF2862) from Bacteroides fragilis NCTC 9343 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical ntf2-like protein
B: Hypothetical ntf2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,54214
Polymers62,3812
Non-polymers1,16112
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical ntf2-like protein
hetero molecules

B: Hypothetical ntf2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,54214
Polymers62,3812
Non-polymers1,16112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
Buried area4760 Å2
ΔGint-5 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.485, 80.485, 196.096
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUGGESTS A DIMER IN SOLUTION, THE BIOLOGICAL SIGNIFICANCE OF THE DIMER IS NOT CLEAR.

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Components

#1: Protein Hypothetical ntf2-like protein


Mass: 31190.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF2862 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LBG4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT (RESIDUES 25-284) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THE CONSTRUCT (RESIDUES 25-284) WAS EXPRESSED WITH AN N-TERMINAL 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.9458.15THE CRYSTAL USED FOR 2 WAVELENGTH MAD PHASING DIFFRACTED TO 2.4 A RESOLUTION. DATA FROM ANOTHER CRYSTAL DIFFRACTING TO 2.15 A WAS USED FOR REFINEMENT.
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30.0% Glycerol, 5.6% polyethylene glycol 4000, 1.0M lithium chloride, 0.1M sodium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL14-111
SYNCHROTRONSSRL BL9-220.91162,0.97930
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDMar 25, 2011Vertical focusing mirror; double crystal Si(111) monochromator
MARMOSAIC 325 mm CCD2CCDMar 11, 2011double crystal monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)MADMx-ray1
2double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.911621
30.97931
ReflectionResolution: 2.15→29.591 Å / Num. all: 38981 / Num. obs: 38981 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rsym value: 0.072 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.215.70.81821646328650.818100
2.21-2.275.70.7072.41601928010.707100
2.27-2.335.80.5273.11565627170.527100
2.33-2.45.80.4133.91531826590.413100
2.4-2.485.80.3454.61480225690.345100
2.48-2.575.80.2825.61433724820.282100
2.57-2.675.80.2176.91397024170.217100
2.67-2.785.80.1768.51335623160.176100
2.78-2.95.80.12911.21285622080.129100
2.9-3.045.80.113.61220821110.1100
3.04-3.215.80.08216.11169220190.082100
3.21-3.45.80.068201092918990.068100
3.4-3.635.80.0723.11036617980.07100
3.63-3.935.80.06625.3965216720.066100
3.93-4.35.80.04927.9886515320.049100
4.3-4.815.80.04131.7815614070.041100
4.81-5.555.80.05741711012260.057100
5.55-6.85.70.05254.2599610450.052100
6.8-9.625.70.02965.646448100.029100
9.62-29.5915.20.02771.822414280.02792.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
BUSTER-TNT2.8.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.591 Å / Cor.coef. Fo:Fc: 0.9611 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. GOL, PEG MODELED ARE PRESENT IN PROTEIN/ CRYSTALLIZATION/ CRYO CONDITIONS. 4. NON-CRYSTALLOGRAPHIC RESTRAINTS WERE APPLIED DURING REFINEMENT (LSSR). 5. THE STRUCTURE WAS SOLVED BASED ON MAD PHASES OF ANOTHER CRYSTAL. REFINEMENT WAS RESTRAINED BY EXPERIMENTAL PHASES. 6. THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION. ALL LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY) EXCEPT LYSINE 250 WHICH APPEARS TO HAVE BEEN PROTECTED FROM METHYLATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 1951 5.01 %RANDOM
Rwork0.1762 ---
obs0.1769 38908 --
Displacement parametersBiso max: 173.07 Å2 / Biso mean: 66.4605 Å2 / Biso min: 28.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.4835 Å20 Å20 Å2
2---1.4835 Å20 Å2
3---2.9669 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 76 158 4070
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1800SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes133HARMONIC2
X-RAY DIFFRACTIONt_gen_planes594HARMONIC5
X-RAY DIFFRACTIONt_it4119HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion505SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4389SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4119HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5592HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion2.79
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2074 150 5.26 %
Rwork0.2074 2703 -
all0.2074 2853 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.99620.3398-1.66651.13030.97063.48-0.44710.0377-0.70660.0707-0.0054-0.14490.54780.03470.4525-0.12260.07820.146-0.20470.0334-0.081220.194522.5016-28.8527
23.4339-0.22280.5062.4842-1.14892.6024-0.112-0.07890.18120.10210.07830.4301-0.2643-0.55240.0337-0.25280.0087-0.0251-0.00990.0153-0.199638.147931.60147.9583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|55 - 284 }A55 - 284
2X-RAY DIFFRACTION2{ B|55 - 284 }B55 - 284

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