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- PDB-2yh5: Structure of the C-terminal domain of BamC -

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Basic information

Entry
Database: PDB / ID: 2yh5
TitleStructure of the C-terminal domain of BamC
ComponentsDAPX PROTEIN
KeywordsLIPID BINDING PROTEIN / LIPOPROTEIN / BAM COMPLEX
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell surface / identical protein binding / membrane
Similarity search - Function
Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / TATA-Binding Protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Outer membrane protein assembly factor BamC / DapX protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.25 Å
AuthorsZeth, K. / Albrecht, R.
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 1.2Feb 5, 2014Group: Refinement description
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: DAPX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0883
Polymers13,8981
Non-polymers1902
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.740, 59.120, 31.060
Angle α, β, γ (deg.)90.00, 116.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DAPX PROTEIN / BAMC


Mass: 13898.449 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-143
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: Q47548, UniProt: P0A903*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SEQUENCE WAS ASSIGNED DUE TO SUBTILISIN TREATMENT AND X-RAY DATA

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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: 1.72 Å3/Da / Density % sol: 27.78 % / Description: NONE
Crystal growpH: 6.5 / Details: 25% PEG1000, 0.1 M MES PH 6.5

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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: 1.28→1.31 Å / Num. obs: 25297 / % possible obs: 98.4 % / Observed criterion σ(I): 2.1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.3
Reflection shellResolution: 1.28→1.31 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
SHARPphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 1.25→29.56 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAAIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18387 1332 5 %RANDOM
Rwork0.14643 ---
obs0.14828 25297 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: 13.829 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.13 Å2
2--0.48 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 10 60 986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022973
X-RAY DIFFRACTIONr_bond_other_d0.0050.02633
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.9741333
X-RAY DIFFRACTIONr_angle_other_deg1.19731569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.34726.04743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57115164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.244154
X-RAY DIFFRACTIONr_chiral_restr0.1570.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02176
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_it2.8841.5619
X-RAY DIFFRACTIONr_mcbond_other0.9511.5250
X-RAY DIFFRACTIONr_mcangle_it4.32521002
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.293354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.1194.5325
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.58231606
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 98 -
Rwork0.251 1852 -
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)
10.19370.1203-0.03570.3904-0.69571.4455-0.0158-0.02090.1205-0.0866-0.04530.02830.18050.02820.06110.090.00040.01550.0725-0.00950.09425.62225.3463.726
20.99040.0469-0.08780.8036-0.54382.25660.05-0.01140.08390.05330.02680.0625-0.0611-0.1834-0.07680.05060.02880.00890.07650.00870.0562-3.59730.5211.474
30.7136-0.0085-0.43350.5618-0.0231.2965-0.00570.0331-0.05940.0662-0.0304-0.0164-0.0489-0.06020.03610.04380.0073-0.00240.0457-0.00930.07473.54725.76715.6
45.29792.35050.88031.80731.47642.4755-0.08240.1905-0.08590.04740.010.03510.1350.06210.07230.06890.020.00620.0505-0.00810.05116.12920.65713.066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A202 - 227
2X-RAY DIFFRACTION2A228 - 249
3X-RAY DIFFRACTION3A250 - 297
4X-RAY DIFFRACTION4A298 - 320

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