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- PDB-4imm: The crystal structure of BamB from Moraxella catarrhalis -

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Basic information

Entry
Database: PDB / ID: 4imm
TitleThe crystal structure of BamB from Moraxella catarrhalis
ComponentsOuter membrane assembly lipoprotein YfgL
KeywordsCHAPERONE / 8-bladed beta-propeller / Protein-protein interactions
Function / homology
Function and homology information


Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / metal ion binding
Similarity search - Function
Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamB / Pyrrolo-quinoline quinone repeat / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsAgnew, C.R.J. / Brady, R.L.
CitationJournal: To be Published
Title: The crystal structure of translocation complex component BamB from Moraxella catarrhalis
Authors: Agnew, C.R.J. / Brady, R.L.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane assembly lipoprotein YfgL
B: Outer membrane assembly lipoprotein YfgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,25312
Polymers84,9702
Non-polymers28210
Water1,62190
1
A: Outer membrane assembly lipoprotein YfgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6879
Polymers42,4851
Non-polymers2028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer membrane assembly lipoprotein YfgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5653
Polymers42,4851
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.300, 78.620, 70.990
Angle α, β, γ (deg.)90.00, 92.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer membrane assembly lipoprotein YfgL


Mass: 42485.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Strain: RH4 / Gene: yfgL, MCR_1168 / Plasmid: pOPINE / Production host: Escherichia coli (E. coli) / References: UniProt: D5VCM9
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M MES, pH6.5 1M Imidazole 0.03M Magnesium chloride 0.03M Calcium chloride 32% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.33→41.544 Å / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.117 / Net I/σ(I): 15
Reflection shellResolution: 2.33→2.45 Å / % possible all: 99

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→41.544 Å / SU ML: 0.28 / σ(F): 1.33 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 3031 5.06 %Random
Rwork0.1889 ---
all0.19 ---
obs0.1916 59898 99.39 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→41.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 10 90 4950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144945
X-RAY DIFFRACTIONf_angle_d1.0876736
X-RAY DIFFRACTIONf_dihedral_angle_d12.9811712
X-RAY DIFFRACTIONf_chiral_restr0.068806
X-RAY DIFFRACTIONf_plane_restr0.004852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.36650.33691040.2722493X-RAY DIFFRACTION94
2.3665-2.40530.30851110.26672510X-RAY DIFFRACTION98
2.4053-2.44670.30521250.24872618X-RAY DIFFRACTION99
2.4467-2.49120.30911460.25032560X-RAY DIFFRACTION99
2.4912-2.53910.2851670.2372600X-RAY DIFFRACTION100
2.5391-2.5910.30851380.22552557X-RAY DIFFRACTION100
2.591-2.64730.29391460.22192610X-RAY DIFFRACTION100
2.6473-2.70890.28871140.21932632X-RAY DIFFRACTION100
2.7089-2.77660.26141490.21182562X-RAY DIFFRACTION100
2.7766-2.85160.27681460.20412628X-RAY DIFFRACTION100
2.8516-2.93550.30151110.21672643X-RAY DIFFRACTION100
2.9355-3.03030.28771410.20922547X-RAY DIFFRACTION100
3.0303-3.13850.26981520.20752593X-RAY DIFFRACTION100
3.1385-3.26410.27521540.19812598X-RAY DIFFRACTION100
3.2641-3.41260.21471260.17672611X-RAY DIFFRACTION100
3.4126-3.59250.2611310.18082572X-RAY DIFFRACTION100
3.5925-3.81740.21621500.17742560X-RAY DIFFRACTION100
3.8174-4.11190.17271450.15912640X-RAY DIFFRACTION100
4.1119-4.52520.20331300.14072565X-RAY DIFFRACTION100
4.5252-5.1790.20911640.15682587X-RAY DIFFRACTION100
5.179-6.52090.21861560.18152587X-RAY DIFFRACTION100
6.5209-41.55040.20811250.17622594X-RAY DIFFRACTION99

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