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- PDB-3sns: Crystal structure of the C-terminal domain of Escherichia coli li... -

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Basic information

Entry
Database: PDB / ID: 3sns
TitleCrystal structure of the C-terminal domain of Escherichia coli lipoprotein BamC
ComponentsLipoprotein 34
KeywordsPROTEIN TRANSPORT / alpha/beta / bacterial outer membrane protein assembly / BAM complex proteins / E. coli outer membrane / lipid anchored outer membrane protein
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 / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / 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
Outer membrane protein assembly factor BamC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, K.H. / Aulakh, S. / Tan, W. / Paetzel, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallographic analysis of the C-terminal domain of the Escherichia coli lipoprotein BamC.
Authors: Kim, K.H. / Aulakh, S. / Tan, W. / Paetzel, M.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Lipoprotein 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9273
Polymers12,8561
Non-polymers712
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.850, 78.850, 52.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Lipoprotein 34 / BamC


Mass: 12856.271 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 224-343)
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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium chloride, 0.1 M HEPES, pH 6.5, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98058 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 11, 2011
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98058 Å / Relative weight: 1
ReflectionResolution: 1.5→41.82 Å / Num. all: 19576 / Num. obs: 19576 / % possible obs: 99.7 % / Observed criterion σ(I): 5 / Redundancy: 5.7 % / Rmerge(I) obs: 0.075 / Rsym value: 0.034 / Net I/σ(I): 10.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2877 / Rsym value: 0.176 / % possible all: 100

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Processing

Software
NameVersionClassification
MxData Collectordata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YH5

2yh5


Resolution: 1.5→41.82 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.54 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18321 999 5.1 %RANDOM
Rwork0.16085 ---
obs0.16195 18558 99.59 %-
all-19576 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 2 99 1002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022950
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9541298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53526.22245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43315158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.57154
X-RAY DIFFRACTIONr_chiral_restr0.1360.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021734
X-RAY DIFFRACTIONr_mcbond_it1.7811.5607
X-RAY DIFFRACTIONr_mcangle_it2.6732980
X-RAY DIFFRACTIONr_scbond_it3.7313343
X-RAY DIFFRACTIONr_scangle_it5.6464.5310
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 74 -
Rwork0.267 1390 -
obs-16027 99.59 %
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)
1-1.86570.0333-4.19811.54184.024913.1094-0.04610.4621-0.02570.1722-0.2086-0.00340.6986-0.98820.25470.0558-0.06760.03270.2825-0.04620.1034-25.616214.35988.8512
23.46492.8721-5.31265.5359-6.494417.4823-0.03960.11890.2462-0.11870.13220.3073-0.082-1.5622-0.09260.0675-0.0403-0.04830.2572-0.05740.0727-23.334212.5182-7.6333
32.41871.81150.21771.4714-1.66986.12110.0436-0.12770.2063-0.13480.04320.1428-0.0843-0.6816-0.08680.1668-0.0198-0.02760.1684-0.01150.125-20.740714.8055-9.0495
40.4081-0.25290.06161.66680.08231.1802-0.0684-0.043-0.02110.08120.05820.0044-0.0781-0.15970.01010.09080.01450.00070.10740.00060.1061-14.565119.18024.8988
52.5226-1.6912-3.15339.10581.03697.3289-0.0853-0.2532-0.06150.2795-0.04010.0670.2842-0.16410.12540.1412-0.0033-0.01270.0906-0.00210.1483-9.177.11716.613
60.9695-2.16120.16377.5843-1.59772.4718-0.04840.01190.02570.1389-0.0308-0.2102-0.16670.14350.07920.1077-0.0155-0.01880.0764-0.00850.1422-4.430620.13180.4903
70.54920.75180.0035.026-1.3950.9441-0.0085-0.0912-0.10830.1480.01840.03880.1248-0.0241-0.00990.12530.00730.02050.06460.00450.1325-9.20874.27772.3734
814.2325-5.232310.162220.34310.16983.4935-0.3619-1.1461-2.10741.36111.13322.1243-0.4145-0.5557-0.77130.06570.05260.19930.17560.2040.382-18.7882-2.55367.9672
98.63942.56620.20985.0864-1.1024-0.6153-0.00230.0911-0.2202-0.24620.09190.03620.2094-0.0318-0.08970.1805-0.0189-0.05260.027-0.01110.1118-10.7181-0.0816-3.2456
104.037-7.26542.345512.0833-2.82033.49560.15890.13570.1234-0.2624-0.1945-0.38620.23130.2310.03560.11170.01120.01440.08730.0060.1689-7.19811.5755-5.2866
112.7101-4.9792-4.53848.4782.10819.08310.22860.5532-0.1618-0.2833-0.1650.3962-0.4422-1.254-0.06360.09120.0997-0.05060.2111-0.02650.0932-21.328523.1426-3.49
122.8625-0.16030.60455.9713-0.5697.70320.04960.0791-0.1537-0.41520.0119-0.57650.72420.4134-0.06150.14540.00150.0070.0884-0.01990.1299-9.978411.2083-8.8904
1320.703215.2396-4.662615.6472-2.043613.2804-0.32430.7295-0.2066-0.96120.49290.14180.3547-0.2924-0.16860.235-0.0233-0.0550.0549-0.01840.0907-14.35246.1108-12.77
140.8641-2.01710.19576.58657.173512.66490.459-0.2202-0.523-0.6943-0.44720.70210.3737-0.6443-0.01180.2498-0.1567-0.19930.09110.03870.1965-19.78364.2062-5.1423
152.02710.63922.673715.13345.123112.565-0.08350.1065-0.06130.45930.13690.65490.2266-0.7247-0.05340.0609-0.07210.00230.1330.03590.1353-19.73588.81545.3316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A224 - 229
2X-RAY DIFFRACTION2A230 - 235
3X-RAY DIFFRACTION3A236 - 245
4X-RAY DIFFRACTION4A246 - 259
5X-RAY DIFFRACTION5A260 - 265
6X-RAY DIFFRACTION6A266 - 272
7X-RAY DIFFRACTION7A273 - 288
8X-RAY DIFFRACTION8A289 - 294
9X-RAY DIFFRACTION9A295 - 301
10X-RAY DIFFRACTION10A302 - 306
11X-RAY DIFFRACTION11A307 - 314
12X-RAY DIFFRACTION12A315 - 323
13X-RAY DIFFRACTION13A324 - 328
14X-RAY DIFFRACTION14A329 - 336
15X-RAY DIFFRACTION15A337 - 343

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