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- PDB-3rwx: Crystal structure of a putative outer membrane protein (BF2706) f... -

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Basic information

Entry
Database: PDB / ID: 3rwx
TitleCrystal structure of a putative outer membrane protein (BF2706) from Bacteroides fragilis NCTC 9343 at 2.40 A resolution
ComponentsHypothetical bacterial outer membrane protein
KeywordsTRANSPORT PROTEIN / Transmembrane beta-barrel / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLipocalin - #340 / Lipocalin - #350 / Calycin-like beta-barrel domain / Lipocalin-like domain / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta / Lipoprotein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical bacterial outer membrane protein (BF2706) from Bacteroides fragilis NCTC 9343 at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 16, 2011Group: Structure summary
Revision 1.4Dec 24, 2014Group: Structure summary
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6Feb 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 bacterial outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,49210
Polymers28,6551
Non-polymers8379
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.154, 154.154, 40.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypothetical bacterial outer membrane protein / Putative lipoprotein


Mass: 28654.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF2706 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LBW6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING GLY 0 FOLLOWED BY RESIDUES 24-283 OF 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: 4.81 Å3/Da / Density % sol: 74.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M potassium sodium tartrate, 2.0M ammonium sulfate, 0.1M sodium citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.96109,0.97934,0.97908
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 25, 2011
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961091
20.979341
30.979081
ReflectionResolution: 2.4→29.816 Å / Num. obs: 21589 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.034 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.490.6721.812473426896.7
2.49-2.580.5662.110714366398.1
2.58-2.70.4232.812459421997.9
2.7-2.840.3133.711814404998.4
2.84-3.020.2125.412235420799
3.02-3.250.1378.212033412999.3
3.25-3.580.07813.712203418599.1
3.58-4.090.05418.512047412298.7
4.09-5.140.03725.912045414699.1
5.140.03526.112183416697.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.816 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 10.206 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.192
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. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 4. GLYCEROL (GOL) USED AS A CRYOPROTECTANT AND SULFATE (SO4) FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 5.THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION AND LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY).
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1107 5.1 %RANDOM
Rwork0.1984 ---
obs0.2006 21577 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.38 Å2 / Biso mean: 33.2552 Å2 / Biso min: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.54 Å20 Å2
2--1.09 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 52 113 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212078
X-RAY DIFFRACTIONr_bond_other_d0.0010.021331
X-RAY DIFFRACTIONr_angle_refined_deg1.5182.0392834
X-RAY DIFFRACTIONr_angle_other_deg0.8333329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69127.17978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98615277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.802152
X-RAY DIFFRACTIONr_chiral_restr0.080.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02347
X-RAY DIFFRACTIONr_mcbond_it0.6381.51296
X-RAY DIFFRACTIONr_mcbond_other0.1191.5537
X-RAY DIFFRACTIONr_mcangle_it1.31622129
X-RAY DIFFRACTIONr_scbond_it2.2663782
X-RAY DIFFRACTIONr_scangle_it3.9244.5691
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 78 -
Rwork0.326 1490 -
all-1568 -
obs--99.24 %
Refinement TLS params.Method: refined / Origin x: -3.7376 Å / Origin y: 64.5712 Å / Origin z: 18.9293 Å
111213212223313233
T0.0714 Å2-0.0086 Å20.018 Å2-0.0789 Å2-0.0054 Å2--0.0119 Å2
L1.2861 °21.2738 °20.1648 °2-1.6515 °20.1112 °2--0.2133 °2
S-0.0482 Å °0.0351 Å °-0.0523 Å °-0.0231 Å °0.0511 Å °-0.0077 Å °0.05 Å °-0.0138 Å °-0.0029 Å °

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