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- PDB-3tgo: Crystal structure of the E. coli BamCD complex -

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Basic information

Entry
Database: PDB / ID: 3tgo
TitleCrystal structure of the E. coli BamCD complex
Components
  • Lipoprotein 34
  • UPF0169 lipoprotein yfiO
KeywordsMEMBRANE PROTEIN / lipoprotein complex / TPR repeat / helix-grip fold / Outer membrane protein assembly / outer membrane
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Secretion of toxins / protein insertion into membrane / cell outer membrane / cell surface / membrane / identical protein binding
Similarity search - Function
Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #50 / : / Outer membrane protein assembly factor BamC-like N-terminal domain / Outer membrane protein assembly factor BamC / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / Outer membrane protein assembly factor BamC-like C-terminal domain / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein ...Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #50 / : / Outer membrane protein assembly factor BamC-like N-terminal domain / Outer membrane protein assembly factor BamC / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / Outer membrane protein assembly factor BamC-like C-terminal domain / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPaetzel, M. / Kim, K.H. / Aulakh, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of the beta-barrel assembly machinery BamCD protein complex
Authors: Kim, K.H. / Aulakh, S. / Paetzel, M.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_conn.ptnr2_label_seq_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: UPF0169 lipoprotein yfiO
B: UPF0169 lipoprotein yfiO
C: Lipoprotein 34
D: Lipoprotein 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,23812
Polymers121,6774
Non-polymers5618
Water2,234124
1
A: UPF0169 lipoprotein yfiO
C: Lipoprotein 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0655
Polymers60,8392
Non-polymers2263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-29 kcal/mol
Surface area19620 Å2
MethodPISA
2
B: UPF0169 lipoprotein yfiO
D: Lipoprotein 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1737
Polymers60,8392
Non-polymers3355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-32 kcal/mol
Surface area20110 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-74 kcal/mol
Surface area37500 Å2
MethodPISA
4
A: UPF0169 lipoprotein yfiO
B: UPF0169 lipoprotein yfiO
C: Lipoprotein 34
D: Lipoprotein 34
hetero molecules

A: UPF0169 lipoprotein yfiO
B: UPF0169 lipoprotein yfiO
C: Lipoprotein 34
D: Lipoprotein 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,47724
Polymers243,3558
Non-polymers1,12216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area33890 Å2
ΔGint-193 kcal/mol
Surface area67640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.780, 133.380, 144.992
Angle α, β, γ (deg.)90.00, 100.15, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein UPF0169 lipoprotein yfiO


Mass: 26127.152 Da / Num. of mol.: 2 / Fragment: UNP residues 21-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2595, JW2577, yfiO / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC02
#2: Protein Lipoprotein 34


Mass: 34711.578 Da / Num. of mol.: 2 / Fragment: UNP residues 26-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2477, dapX, JW2462, nlpB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A903

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Non-polymers , 6 types, 132 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.86 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 295 K / pH: 9.2
Details: 0.2 M K2HPO4 and 20% PEG3350, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2009
Details: MERIDIONALLY-BENT FUSED SILICA MIRROR WITH PALLADIUM AND UNCOATED STRIPES VERTICALLY- FOCUSING AT 6.6:1 DEMAGNIFICATION
RadiationMonochromator: DOUBLE SILICON(111) CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→97.5 Å / Num. obs: 30529 / % possible obs: 99.6 % / Observed criterion σ(I): 5 / Redundancy: 7.2 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 5.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YH6 AND 2YHC

2yh6

2yhc


Resolution: 2.9→97.45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.879 / SU B: 12.099 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.758 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1538 5 %RANDOM
Rwork0.177 ---
obs0.181 28975 99.5 %-
all-30529 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å21.96 Å2
2---1.51 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.9→97.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 32 124 6454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226468
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9721.9598798
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79124.585325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.733151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4081549
X-RAY DIFFRACTIONr_chiral_restr0.0810.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215036
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_it1.0541.54017
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02826450
X-RAY DIFFRACTIONr_scbond_it2.90632451
X-RAY DIFFRACTIONr_scangle_it4.9234.52346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 136 -
Rwork0.213 2109 -
obs--99.69 %

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