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- PDB-6fsu: Crystal structure of E.coli BamA beta-barrel with a C-terminal ex... -

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Basic information

Entry
Database: PDB / ID: 6fsu
TitleCrystal structure of E.coli BamA beta-barrel with a C-terminal extension
ComponentsOuter membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane
Similarity search - Function
membrane protein fhac: a member of the omp85/tpsb transporter family / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin ...membrane protein fhac: a member of the omp85/tpsb transporter family / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZahn, M. / Hartmann, J.-B. / Hiller, S.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Sequence-Specific Solution NMR Assignments of the beta-Barrel Insertase BamA to Monitor Its Conformational Ensemble at the Atomic Level.
Authors: Hartmann, J.B. / Zahn, M. / Burmann, I.M. / Bibow, S. / Hiller, S.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)94,0602
Polymers94,0602
Non-polymers00
Water95553
1
A: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)47,0301
Polymers47,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)47,0301
Polymers47,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.737, 159.378, 55.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 412 - 819 / Label seq-ID: 13 - 420

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 47029.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: bamA, yaeT, Z0188, ECs0179 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A942
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22 % (w/v) PEG 400, 0.07 M NaCl, 0.05 M sodium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→66.84 Å / Num. obs: 34607 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.111 / Net I/σ(I): 7.7
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4151 / CC1/2: 0.647 / Rpim(I) all: 0.768 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N75

4n75


Resolution: 2.6→66.84 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU B: 35.924 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R: 0.626 / ESU R Free: 0.343 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29779 1747 5.1 %RANDOM
Rwork0.26901 ---
obs0.27052 32803 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.603 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--4.85 Å20 Å2
3----4.93 Å2
Refinement stepCycle: 1 / Resolution: 2.6→66.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 0 53 6195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026330
X-RAY DIFFRACTIONr_bond_other_d0.0020.025264
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.9218613
X-RAY DIFFRACTIONr_angle_other_deg1.135312248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0995771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62124.468329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85115909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9551522
X-RAY DIFFRACTIONr_chiral_restr0.1280.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217299
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021447
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_it1.0641.993096
X-RAY DIFFRACTIONr_mcbond_other1.0641.993095
X-RAY DIFFRACTIONr_mcangle_it1.8632.9823863
X-RAY DIFFRACTIONr_mcangle_other1.8632.9823864
X-RAY DIFFRACTIONr_scbond_it1.0692.1363234
X-RAY DIFFRACTIONr_scbond_other1.0692.1363233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.853.1574750
X-RAY DIFFRACTIONr_long_range_B_refined3.49922.2766942
X-RAY DIFFRACTIONr_long_range_B_other3.49822.2736941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24394 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 110 -
Rwork0.392 2415 -
obs--99.76 %
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)
12.5197-0.1224-0.39681.08940.21071.8255-0.0585-0.15880.03090.1193-0.0376-0.0177-0.0663-0.37530.09610.05350.009-0.00820.1049-0.02110.2977-2.794952.806321.4623
23.05660.95861.22681.70151.68293.26640.00850.06590.25850.0841-0.05050.1309-0.15650.23560.04190.0865-0.03310.0610.06130.02510.239213.19654.736322.4196
32.30740.0853-0.11831.36890.30592.53820.0813-0.07570.3657-0.0371-0.0585-0.0234-0.63520.0512-0.02280.182-0.03030.03580.02240.01360.320612.560866.441115.0844
42.4319-0.45590.36910.8861-0.64381.6883-0.0082-0.2479-0.07260.2227-0.05040.01010.16220.46090.05860.14870.0858-0.0080.18830.03250.302231.872126.633923.6809
52.48590.2271-0.20331.5033-0.39962.00360.06690.0528-0.21160.0143-0.0617-0.02090.2535-0.0408-0.00520.0674-0.0049-0.07630.0137-0.03670.281616.398921.135416.0632
61.1920.321-0.50011.285-0.11882.02940.0920.0599-0.48660.03710.01450.07410.63440.0715-0.10650.29220.0069-0.09510.0946-0.02420.455416.497311.29617.3982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A412 - 559
2X-RAY DIFFRACTION2A560 - 635
3X-RAY DIFFRACTION3A636 - 819
4X-RAY DIFFRACTION4B412 - 548
5X-RAY DIFFRACTION5B549 - 731
6X-RAY DIFFRACTION6B732 - 819

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