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- PDB-3prw: Crystal structure of the lipoprotein BamB -

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Basic information

Entry
Database: PDB / ID: 3prw
TitleCrystal structure of the lipoprotein BamB
ComponentsLipoprotein yfgL
KeywordsSTRUCTURAL PROTEIN / beta propeller
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / membrane / identical protein binding
Similarity search - Function
PQQ enzyme repeat / Outer membrane protein assembly factor BamB / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.8 Å
AuthorsHeuck, A. / Clausen, T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Augmenting beta-augmentation: structural basis of how BamB binds BamA and may support folding of outer membrane proteins.
Authors: Heuck, A. / Schleiffer, A. / Clausen, T.
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein yfgL


Theoretical massNumber of molelcules
Total (without water)40,1911
Polymers40,1911
Non-polymers00
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.221, 120.967, 134.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

21A-770-

HOH

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Components

#1: Protein Lipoprotein yfgL / Protein assembly complex / lipoprotein component


Mass: 40190.688 Da / Num. of mol.: 1 / Fragment: UNP Residues 21-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yfgL, b2512, JW2496 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77774
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM Tris, pH 6.9, 20% PEG 3350, 200 mM ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.96 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Av σ(I) over netI: 7 / Number: 150488 / Rsym value: 0.058 / D res high: 1.8 Å / D res low: 89.493 Å / Num. obs: 37222 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.6921.9595.710.0390.0393.9
4.035.6999.110.0460.0464.1
3.294.0397.110.0450.0454
2.853.2998.110.0470.0474
2.552.8599.310.0540.0544.3
2.322.5597.710.0660.0664.1
2.152.3298.310.0820.0823.9
2.012.1599.210.1160.1164.1
1.92.0199.710.1580.1584.2
1.81.997.610.2380.2383.8
ReflectionResolution: 1.8→17.3 Å / Num. obs: 37883 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.34 / Redundancy: 6 % / Rmerge(I) obs: 0.049 / Rsym value: 0.045 / Net I/σ(I): 27.4
Reflection shellResolution: 1.8→17.3 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 16.7 / Rsym value: 0.072 / % possible all: 99.6

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.821.9500339672979
ANO_11.821.950.8380337340
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_17.58-21.9500378155
ISO_15.53-7.5800654145
ISO_14.56-5.5300879152
ISO_13.97-4.56001054154
ISO_13.56-3.97001191151
ISO_13.26-3.56001281132
ISO_13.02-3.26001434152
ISO_12.83-3.02001549151
ISO_12.67-2.83001654145
ISO_12.54-2.67001771150
ISO_12.42-2.54001869150
ISO_12.32-2.42001896135
ISO_12.23-2.32002009154
ISO_12.15-2.23002119141
ISO_12.08-2.15002180150
ISO_12.01-2.08002282151
ISO_11.95-2.01002352172
ISO_11.9-1.95002445161
ISO_11.85-1.9002471140
ISO_11.8-1.85002499138
ANO_17.58-21.952.96103780
ANO_15.53-7.582.05306500
ANO_14.56-5.531.6308750
ANO_13.97-4.561.519010520
ANO_13.56-3.971.49011870
ANO_13.26-3.561.183012670
ANO_13.02-3.261.204014210
ANO_12.83-3.021.205015440
ANO_12.67-2.831.153016490
ANO_12.54-2.670.925017650
ANO_12.42-2.540.79018680
ANO_12.32-2.420.606018740
ANO_12.23-2.320.518019860
ANO_12.15-2.230.438021110
ANO_12.08-2.150.358021680
ANO_12.01-2.080.281022600
ANO_11.95-2.010.258023410
ANO_11.9-1.950.229024310
ANO_11.85-1.90.187024510
ANO_11.8-1.850.162024560
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
146.22995.20379.837SE41.191.54
245.55464.25586.901SE44.511.47
326.29462.86492.685SE28.641.41
448.18288.87367.105SE34.431.41
533.025102.886120.513SE38.261.18
615.13517.47122.405SE43.50.39
71.012120.683108.679SE36.370.17

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SOLOMONphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
RemDAqdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.8→9.995 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8706 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.7 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 1870 4.94 %RANDOM
Rwork0.1833 ---
obs0.1844 37881 99.51 %-
all-38123 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.037 Å2 / ksol: 0.453 e/Å3
Displacement parametersBiso max: 86.54 Å2 / Biso mean: 23.2845 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.1529 Å2-0 Å20 Å2
2---2.0563 Å20 Å2
3---1.9034 Å2
Refinement stepCycle: LAST / Resolution: 1.8→9.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2669 0 0 431 3100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072718
X-RAY DIFFRACTIONf_angle_d1.1453707
X-RAY DIFFRACTIONf_chiral_restr0.083432
X-RAY DIFFRACTIONf_plane_restr0.004481
X-RAY DIFFRACTIONf_dihedral_angle_d18.235941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.86390.24372000.189535573757100
1.8639-1.9380.22431510.19473564371599
1.938-2.02560.23481890.195835533742100
2.0256-2.13140.22931840.194735863770100
2.1314-2.26350.21332030.191135733776100
2.2635-2.43590.22252010.191635753776100
2.4359-2.67670.2221770.191236423819100
2.6767-3.05440.2091890.18833544373398
3.0544-3.81230.17241860.166336673853100
3.8123-9.99490.17511900.16833750394099

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