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- PDB-3q7o: The crystal structure of BamB from the BAM complex in spacegroup P213 -

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Basic information

Entry
Database: PDB / ID: 3q7o
TitleThe crystal structure of BamB from the BAM complex in spacegroup P213
ComponentsLipoprotein yfgL
KeywordsPROTEIN BINDING / beta-propeller / BAM complex / outer membrane protein folding / Gram negative / BamA
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
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: 2.091 Å
AuthorsNoinaj, N. / Fairman, J.W. / Buchanan, S.K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure of BamB Suggests Interactions with BamA and Its Role within the BAM Complex.
Authors: Noinaj, N. / Fairman, J.W. / Buchanan, S.K.
History
DepositionJan 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)40,0961
Polymers40,0961
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.145, 103.145, 103.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

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Components

#1: Protein Lipoprotein yfgL / BamB


Mass: 40095.609 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) / Gene: yfgL, b2512, JW2496 / Production host: Escherichia coli (E. coli) / References: UniProt: P77774
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 1.0 M lithium sulfate, 2% PEG8000, pH 7.5, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2010
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.091→50 Å / Num. all: 21908 / Num. obs: 21844 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rsym value: 0.14 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.61 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_572)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q7M

3q7m


Resolution: 2.091→19.85 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2634 2000 9.17 %
Rwork0.1994 --
obs0.2052 21810 99.7 %
all-21724 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.3648 Å20 Å20 Å2
2--16.3648 Å20 Å2
3---16.3648 Å2
Refinement stepCycle: LAST / Resolution: 2.091→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 0 128 2820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112838
X-RAY DIFFRACTIONf_angle_d1.0243775
X-RAY DIFFRACTIONf_dihedral_angle_d13.731952
X-RAY DIFFRACTIONf_chiral_restr0.063443
X-RAY DIFFRACTIONf_plane_restr0.004492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0911-2.16580.33791960.29451929X-RAY DIFFRACTION99
2.1658-2.25240.42231960.36371956X-RAY DIFFRACTION99
2.2524-2.35470.29111970.28941965X-RAY DIFFRACTION99
2.3547-2.47860.33381980.25241962X-RAY DIFFRACTION100
2.4786-2.63360.31321970.22351959X-RAY DIFFRACTION100
2.6336-2.83640.29922020.22221974X-RAY DIFFRACTION100
2.8364-3.12090.27912050.21021983X-RAY DIFFRACTION100
3.1209-3.57020.21992030.17041992X-RAY DIFFRACTION100
3.5702-4.48950.22032030.15032011X-RAY DIFFRACTION100
4.4895-19.85110.22622030.16012079X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.3397 Å / Origin y: -25.34 Å / Origin z: 12.0207 Å
111213212223313233
T-0.0223 Å20.0643 Å20.0859 Å2--0.1256 Å2-0.0399 Å2---0.082 Å2
L1.2184 °2-0.0524 °20.2097 °2-0.7024 °2-0.3261 °2--1.1356 °2
S-0.1334 Å °0.1484 Å °-0.0017 Å °-0.1033 Å °0.0553 Å °0.0557 Å °-0.0692 Å °0.1982 Å °0.0026 Å °
Refinement TLS groupSelection details: chain A

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