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- PDB-2yh6: Structure of the N-terminal domain of BamC from E. coli -

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Basic information

Entry
Database: PDB / ID: 2yh6
TitleStructure of the N-terminal domain of BamC from E. coli
ComponentsLIPOPROTEIN 34
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell surface / membrane / identical protein binding
Similarity search - Function
Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #50 / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.55 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOPROTEIN 34
B: LIPOPROTEIN 34
C: LIPOPROTEIN 34
D: LIPOPROTEIN 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,70810
Polymers50,1324
Non-polymers5766
Water2,450136
1
C: LIPOPROTEIN 34
D: LIPOPROTEIN 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2584
Polymers25,0662
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-43.1 kcal/mol
Surface area11300 Å2
MethodPISA
2
A: LIPOPROTEIN 34
B: LIPOPROTEIN 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4506
Polymers25,0662
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-28.9 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.577, 46.631, 60.208
Angle α, β, γ (deg.)102.70, 92.86, 118.20
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A4 - 113
2112B4 - 113
3112C4 - 113
4112D4 - 113

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Components

#1: Protein
LIPOPROTEIN 34 / / BAMC


Mass: 12532.893 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 101-212
Source method: isolated from a genetically manipulated source
Details: DOMAIN WAS IDENTIFIED BY LIMITED PROTEOLYSIS / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A903
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DOMAIN WAS IDENTIFIED BY LIMITED PROTEOLYSIS. THEREFORE, THE N- AND C-TERMINUS ARE NOT DEFINED.

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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: 2.21 Å3/Da / Density % sol: 44.24 % / Description: NONE
Crystal growpH: 3.5 / Details: 2 M (NH4)2SO4, 0.1 M CITRIC ACID PH 3.5

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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: 1.55→40 Å / Num. obs: 56570 / % possible obs: 95.1 % / Observed criterion σ(I): 2.7 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 93.8

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Processing

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

Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.907 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 2994 5 %RANDOM
Rwork0.19479 ---
obs0.19676 56570 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.14 Å20.1 Å2
2---0.29 Å20.1 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 30 136 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223483
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.531.9484744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4335437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04325.68169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68415592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4531521
X-RAY DIFFRACTIONr_chiral_restr0.1780.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212617
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_it2.431.52165
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5723482
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.42231318
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.5424.51256
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.03733483
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A134tight positional0.140.05
2B134tight positional0.150.05
3C134tight positional0.150.05
4D134tight positional0.130.05
1A118medium positional0.30.5
2B118medium positional0.250.5
3C118medium positional0.280.5
4D118medium positional0.240.5
1A134tight thermal0.430.5
2B134tight thermal0.440.5
3C134tight thermal0.440.5
4D134tight thermal0.430.5
1A118medium thermal0.412
2B118medium thermal0.372
3C118medium thermal0.432
4D118medium thermal0.422
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 237 -
Rwork0.232 4018 -
obs--93.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.9865-3.2454-1.364712.94440.31365.65110.2261-0.69740.63130.5279-0.15320.1409-0.5093-0.0994-0.07290.1328-0.06410.01160.2901-0.09550.12454.23258.38568.0486
25.0074-0.5374-2.27772.31050.36284.35670.11430.17780.639-0.0739-0.04360.2117-0.1594-0.5218-0.07080.0414-0.0104-0.01560.2840.00470.1366-8.29246.08041.7446
31.8586-0.2821-0.63561.42520.11991.5672-0.0170.0117-0.0205-0.0751-0.0245-0.03350.0749-0.03150.04150.0628-0.0178-0.00540.10490.00610.04051.9224-1.701-1.9845
46.337-2.716-1.808111.11780.43295.9660.041-0.5227-0.3050.3493-0.2405-0.32950.63240.03680.19950.1058-0.0571-0.02210.24380.07520.123214.019-2.12636.3011
56.626-1.18521.47553.82131.01095.01380.17070.3891-0.0818-0.03520.0542-0.29320.18720.5209-0.22490.019-0.0281-0.01030.35560.00860.06926.53262.35411.2951
62.7452-0.51350.10362.42060.25951.33040.03310.03090.1956-0.1082-0.0554-0.0339-0.10930.06390.02230.0768-0.02950.0040.13980.00580.078416.768210.73380.6835
722.95556.15173.80517.06731.88794.56130.12740.6892-0.66-0.36710.1193-0.6825-0.31060.4639-0.24670.31920.0410.06690.0806-0.00310.148710.5468-20.355523.0152
85.0324-2.1410.26624.96191.62725.36-0.0468-0.2414-0.18690.2710.31210.03370.37340.374-0.26530.33820.1318-0.00430.07910.00340.033511.9895-33.821727.6709
92.4458-0.62590.25061.93690.44251.24360.0013-0.1223-0.14710.0077-0.04120.1840.0768-0.0860.03990.1450.01270.00280.06790.00740.0845-0.0227-28.713228.2826
1012.06990.64372.2026.02540.12414.2114-0.20470.458-0.2402-0.98040.05260.63140.0769-0.34810.15210.38940.0675-0.10390.105-0.03570.1364-4.3051-16.932920.7512
112.4848-1.09051.09444.6324-1.32844.188-0.0527-0.0972-0.07880.00010.04520.5921-0.3438-0.38420.00740.25050.1162-0.02730.0808-0.0290.1128-7.6479-4.681627.3225
121.7416-0.1810.50631.4645-0.26121.53810.01-0.0708-0.01930.0097-0.0510.0023-0.05790.0350.0410.10740.00940.00840.0560.00080.03783.7335-9.991830.8417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A77 - 91
2X-RAY DIFFRACTION2A92 - 114
3X-RAY DIFFRACTION3A115 - 187
4X-RAY DIFFRACTION4B77 - 91
5X-RAY DIFFRACTION5B92 - 114
6X-RAY DIFFRACTION6B115 - 188
7X-RAY DIFFRACTION7C77 - 91
8X-RAY DIFFRACTION8C92 - 114
9X-RAY DIFFRACTION9C115 - 187
10X-RAY DIFFRACTION10D77 - 91
11X-RAY DIFFRACTION11D92 - 114
12X-RAY DIFFRACTION12D115 - 188

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