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- PDB-2yh3: The structure of BamB from E. coli -

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Basic information

Entry
Database: PDB / ID: 2yh3
TitleThe structure of BamB from E. coli
ComponentsLIPOPROTEIN YFGL
KeywordsLIPID BINDING PROTEIN / BAM COMPLEX / PROPELLER FOLD
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / identical protein binding / membrane
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAlbrecht, R. / Zeth, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis of Outer Membrane Protein Biogenesis in Bacteria.
Authors: Albrecht, R. / Zeth, K.
History
DepositionApr 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)40,6631
Polymers40,6631
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.841, 101.841, 110.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein LIPOPROTEIN YFGL / BAMB


Mass: 40663.070 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77774
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.53 Å3/Da / Density % sol: 65.12 % / Description: NONE
Crystal growpH: 4.6 / Details: 3.5M NH4CL, 0.1M NA-ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 17551 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.6
Reflection shellResolution: 2.6→2.66 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.903 / SU B: 24.557 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26987 925 5 %RANDOM
Rwork0.21072 ---
obs0.21358 17551 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.593 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 0 67 2782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222765
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.9423773
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2365361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96825.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90415430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.561513
X-RAY DIFFRACTIONr_chiral_restr0.1410.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212101
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9241.51783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75822860
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.493982
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1084.5913
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 67 -
Rwork0.355 1271 -
obs--100 %
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)
13.1758-2.0718-1.96092.9163-0.38215.9126-0.7110.2716-0.4099-0.05020.06050.30590.7404-1.2250.65050.2447-0.47530.04260.4851-0.20720.0678-12.2727.024-7.861
2-5.9743.37565.88325.9952-0.80184.0590.06860.1293-0.1902-0.5803-0.0082-0.05191.1804-0.5354-0.06040.5687-0.2220.14580.147-0.03110.1154-5.90117.1543.68
31.77571.06450.1057-0.1498-0.18982.1119-0.2979-0.2447-0.2118-0.30030.0263-0.07060.6343-0.0350.27150.4941-0.07820.17340.12480.00320.1763-4.14119.09612.123
42.2967-0.3962-0.27210.9922-0.53972.8999-0.1408-0.1849-0.1518-0.0148-0.0628-0.0319-0.00530.23190.20360.26580.02710.04330.25230.0230.07358.99733.10311.921
55.6935-1.1308-0.25250.3217-0.19622.3971-0.1177-0.31410.0974-0.07210.0505-0.1024-0.07770.13590.06710.2695-0.0034-0.00190.2378-0.01210.03959.88640.8953.712
63.80860.08140.49910.8947-1.35142.8645-0.076-0.03320.1778-0.2104-0.0816-0.00710.0854-0.11430.15760.2995-0.01330.00660.1768-0.03670.0537.35640.97-7.653
71.3878-1.60280.72430.8857-0.1583.5613-0.17520.29920.0851-0.2424-0.0129-0.09210.1645-0.42090.18820.3284-0.05090.00660.2206-0.04350.0298-0.48240.825-13.866
83.07230.7284-2.84683.1076-1.67128.5284-0.37270.4168-0.1463-0.33410.0647-0.14910.6513-0.72610.30810.39-0.2199-0.00080.2435-0.13940.0277-7.46130.196-13.233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 45
2X-RAY DIFFRACTION2A46 - 62
3X-RAY DIFFRACTION3A63 - 143
4X-RAY DIFFRACTION4A144 - 199
5X-RAY DIFFRACTION5A200 - 252
6X-RAY DIFFRACTION6A253 - 288
7X-RAY DIFFRACTION7A289 - 309
8X-RAY DIFFRACTION8A310 - 352

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