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- PDB-3q54: Crystal structure of Escherichia coli BamB -

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Basic information

Entry
Database: PDB / ID: 3q54
TitleCrystal structure of Escherichia coli BamB
ComponentsOuter membrane assembly lipoprotein YfgL
KeywordsLIPID BINDING PROTEIN / Lipoprotein / BamB
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.004 Å
AuthorsDong, C. / Hou, H. / Yang, X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of Escherichia coli BamB and its interaction with POTRA domains of BamA.
Authors: Dong, C. / Yang, X. / Hou, H.F. / Shen, Y.Q. / Dong, Y.H.
History
DepositionDec 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane assembly lipoprotein YfgL


Theoretical massNumber of molelcules
Total (without water)39,3181
Polymers39,3181
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.150, 121.123, 133.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein Outer membrane assembly lipoprotein YfgL


Mass: 39317.723 Da / Num. of mol.: 1 / Fragment: UNP residues 25-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: EcDH1_1156 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QPR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Lithium sulfate monohydrate 0.1M BIS-TRIS, pH 6.5, 25%PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 30, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→89 Å / Num. all: 25190 / % possible obs: 78.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.07 Å / % possible all: 60.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.004→29.196 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 1176 5.14 %
Rwork0.1722 --
obs0.1754 22899 84.17 %
all-25190 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.775 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1637 Å20 Å2-0 Å2
2--9.2124 Å20 Å2
3----3.0487 Å2
Refinement stepCycle: LAST / Resolution: 2.004→29.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 0 348 2968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072667
X-RAY DIFFRACTIONf_angle_d1.0713635
X-RAY DIFFRACTIONf_dihedral_angle_d14.365927
X-RAY DIFFRACTIONf_chiral_restr0.074424
X-RAY DIFFRACTIONf_plane_restr0.004470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0042-2.09530.3202810.2111541X-RAY DIFFRACTION49
2.0953-2.20580.2751990.19342283X-RAY DIFFRACTION71
2.2058-2.34390.25921490.21372573X-RAY DIFFRACTION81
2.3439-2.52480.2871420.20372808X-RAY DIFFRACTION88
2.5248-2.77870.28771390.19282905X-RAY DIFFRACTION90
2.7787-3.18040.24121920.19243022X-RAY DIFFRACTION94
3.1804-4.00530.20351830.15413224X-RAY DIFFRACTION99
4.0053-29.19870.2041910.14883367X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.7261 Å / Origin y: 39.0286 Å / Origin z: 45.0395 Å
111213212223313233
T0.0698 Å20.0155 Å2-0.0031 Å2-0.078 Å2-0.0107 Å2--0.0703 Å2
L0.8067 °20.5414 °2-0.0656 °2-0.7988 °2-0.1474 °2--0.3261 °2
S0.0561 Å °-0.0879 Å °0.1379 Å °0.0862 Å °-0.0375 Å °0.089 Å °0.0267 Å °-0.0147 Å °-0.0181 Å °
Refinement TLS groupSelection details: all

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