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- PDB-4raa: Crystal structure of a Putative exported protein (BF0058) from Ba... -

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Basic information

Entry
Database: PDB / ID: 4raa
TitleCrystal structure of a Putative exported protein (BF0058) from Bacteroides fragilis NCTC 9343 at 2.60 A resolution
ComponentsPutative exported protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF16288 family / DUF4934 / 6-bladed beta-propeller of YWTD superfamily / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology6-bladed beta-propeller / Six-bladed beta-propeller, TolB-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / PHOSPHATE ION / Exported protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative exported protein (BF0058) from Bacteroides fragilis NCTC 9343 at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7432
Polymers41,6481
Non-polymers951
Water25214
1
A: Putative exported protein
hetero molecules

A: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4864
Polymers83,2962
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1590 Å2
ΔGint-19 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.800, 55.210, 81.330
Angle α, β, γ (deg.)90.000, 122.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-400-

PO4

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative exported protein


Mass: 41647.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF9343_0057 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LJ40
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 23-383 OF 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.250M di-ammonium hydrogen phosphate, 22.1% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97947,0.97908
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2014
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979471
30.979081
ReflectionResolution: 2.6→61.243 Å / Num. obs: 14464 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 64.928 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.6-2.670.64913110199292.3
2.67-2.740.481.23052197194.7
2.74-2.820.4521.52885186392.4
2.82-2.910.32322853186892.3
2.91-3.010.2812.42449166090.3
3.01-3.110.1873.32751175694.2
3.11-3.230.1394.42658169494.9
3.23-3.360.1195.52469159493
3.36-3.510.0867.42371154992.5
3.51-3.680.0739.32055140289.3
3.68-3.880.05311.22174138794
3.88-4.120.04613.62063133193.9
4.12-4.40.036171893122593.3
4.4-4.750.03118.51773116993.9
4.75-5.210.0319.71633105693.1
5.21-5.820.03617.6156199794
5.82-6.720.04515.5127081993.8
6.72-8.230.02919.5105970790.2
8.23-11.640.023187155691.9
11.640.01439.844528589.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→61.243 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 28.501 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.661 / ESU R Free: 0.316
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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. 5. PHOSPHATE ION (PO4) CRYSTALLIZATION SOLUTION IS MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 728 5 %RANDOM
Rwork0.214 ---
obs0.2162 14460 96.88 %-
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: 82.83 Å2 / Biso mean: 43.0202 Å2 / Biso min: 15.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å2-0 Å2-3.02 Å2
2---1.27 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.6→61.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 5 14 2882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022939
X-RAY DIFFRACTIONr_bond_other_d0.0020.022709
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9693985
X-RAY DIFFRACTIONr_angle_other_deg1.1436251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5385357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31325.306147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60515496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.833158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023352
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02690
X-RAY DIFFRACTIONr_mcbond_it1.1622.6581419
X-RAY DIFFRACTIONr_mcbond_other1.1612.6561418
X-RAY DIFFRACTIONr_mcangle_it1.9514.9791773
LS refinement shellResolution: 2.603→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 55 -
Rwork0.384 1011 -
all-1066 -
obs--96.73 %
Refinement TLS params.Method: refined / Origin x: 23.286 Å / Origin y: 31.932 Å / Origin z: 13.351 Å
111213212223313233
T0.1122 Å20.0026 Å20.1312 Å2-0.4029 Å20.0289 Å2--0.2219 Å2
L1.7799 °2-0.231 °20.3602 °2-0.457 °20.2821 °2--2.2504 °2
S-0.0244 Å °-0.0409 Å °0.0157 Å °0.0876 Å °-0.0056 Å °0.0448 Å °0.0854 Å °0.1868 Å °0.03 Å °

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