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- PDB-5t10: PelC dodecamer from Paraburkholderia phytofirmans, space group P6 -

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Basic information

Entry
Database: PDB / ID: 5t10
TitlePelC dodecamer from Paraburkholderia phytofirmans, space group P6
ComponentsUncharacterized protein
KeywordsSTRUCTURAL PROTEIN / lipoprotein / periplasmic
Function / homologyPenicillin-binding protein activator LpoB / Peptidoglycan-synthase activator LpoB / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesParaburkholderia phytofirmans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4987 Å
AuthorsMarmont, L.S. / Howell, P.L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of Pseudomonas aeruginosa.
Authors: Marmont, L.S. / Rich, J.D. / Whitney, J.C. / Whitfield, G.B. / Almblad, H. / Robinson, H. / Parsek, M.R. / Harrison, J.J. / Howell, P.L.
History
DepositionAug 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)67,2224
Polymers67,2224
Non-polymers00
Water1,40578
1
A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)201,66712
Polymers201,66712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
2
C: Uncharacterized protein
D: Uncharacterized protein

C: Uncharacterized protein
D: Uncharacterized protein

C: Uncharacterized protein
D: Uncharacterized protein

C: Uncharacterized protein
D: Uncharacterized protein

C: Uncharacterized protein
D: Uncharacterized protein

C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)201,66712
Polymers201,66712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Unit cell
Length a, b, c (Å)118.113, 118.113, 85.688
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein
Uncharacterized protein


Mass: 16805.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phytofirmans (bacteria)
Strain: DSM 17436 / LMG 22146 / PsJN / Gene: Bphyt_1493 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2T2U6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1 M NaH2PO4/KHPO4 pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 23687 / % possible obs: 98 % / Redundancy: 21.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 28.5
Reflection shellResolution: 2.499→2.59 Å / Redundancy: 15.8 % / Rmerge(I) obs: 0.759 / % possible all: 87.2

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T11
Resolution: 2.4987→48.626 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.12
RfactorNum. reflection% reflection
Rfree0.2355 1933 8.6 %
Rwork0.185 --
obs0.1895 22479 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4987→48.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 0 78 3956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073937
X-RAY DIFFRACTIONf_angle_d1.0585386
X-RAY DIFFRACTIONf_dihedral_angle_d12.5621314
X-RAY DIFFRACTIONf_chiral_restr0.067659
X-RAY DIFFRACTIONf_plane_restr0.005691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4987-2.56120.35241130.2841215X-RAY DIFFRACTION78
2.5612-2.63040.31711280.2551273X-RAY DIFFRACTION84
2.6304-2.70780.29471230.25431377X-RAY DIFFRACTION90
2.7078-2.79520.31991450.21891434X-RAY DIFFRACTION93
2.7952-2.89510.27491340.2131462X-RAY DIFFRACTION95
2.8951-3.0110.28671320.22251477X-RAY DIFFRACTION97
3.011-3.1480.28671460.2221480X-RAY DIFFRACTION96
3.148-3.3140.28121400.20311525X-RAY DIFFRACTION98
3.314-3.52150.20981420.18291524X-RAY DIFFRACTION99
3.5215-3.79330.22781460.17031526X-RAY DIFFRACTION99
3.7933-4.17490.21861440.14961558X-RAY DIFFRACTION100
4.1749-4.77850.19611430.13441542X-RAY DIFFRACTION100
4.7785-6.01870.22221510.16931559X-RAY DIFFRACTION100
6.0187-48.63550.20111460.19481594X-RAY DIFFRACTION99
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)
10.75761.78560.1425.98912.35512.92570.3845-0.19580.78650.3305-0.51930.6679-0.0944-0.30510.19160.59080.0484-0.14220.3584-0.07691.201560.7101153.8096-5.7956
23.4090.01681.48633.05920.17562.5515-0.0003-0.35650.04860.0295-0.2876-0.37720.020.02160.30740.28160.01860.03150.2922-0.05170.610465.6394141.26810.5334
32.32781.43431.4766.0099-3.36314.50190.5978-1.16010.28122.7535-1.0385-0.07981.03970.4548-0.27411.49340.0646-0.25760.8095-0.25360.689465.5446152.360312.0734
44.1546-0.1712-0.04930.9656-1.2032.93280.45230.137-0.16910.2067-0.9110.15490.5051-0.90490.21180.28730.05020.03590.2868-0.10150.568759.6442132.6892-7.6393
52.41332.32622.93628.33355.8716.0122-0.3348-0.29440.0950.2414-0.38121.01050.1299-0.74720.47190.296-0.07070.03940.38360.09620.633757.5855142.9142-3.5638
64.40752.58461.28113.5406-1.45743.99810.46730.55210.7277-0.4114-0.2272-0.4134-0.5312-0.3197-0.18970.1903-0.0015-0.03820.426-0.00530.846857.7242143.8293-6.7422
71.31721.01730.85616.95993.21544.5450.01270.5220.4061-0.87440.4345-1.5611-0.41950.2989-0.39520.3223-0.02470.02520.33580.03160.706264.2285143.794-10.5069
87.4505-0.5773.38122.71442.45263.95540.21430.13630.4121-0.65070.0543-0.8532-0.07050.1626-0.38830.7249-0.0728-0.14160.4173-0.03191.072285.2588145.1273-6.5138
94.20141.349-0.18334.58271.28832.1402-0.1273-0.6428-0.48290.2692-0.138-0.9136-0.00470.08170.26720.40550.0086-0.0120.3148-0.01240.658384.2629132.7331.4101
103.71310.64770.12938.87551.87334.224-0.0095-0.22260.48450.6357-0.18420.05770.0356-0.18750.27620.34010.04150.030.3275-0.01650.708278.8812136.6564-1.9332
116.56811.80550.13251.8747-2.43274.19820.27110.5236-0.4232-0.7557-0.0208-1.61040.00410.3883-0.30890.29350.02750.04270.3660.01610.44383.9206134.1852-12.1857
125.4097-2.23520.82956.1659-3.27621.35930.21590.07440.49080.2251-0.4260.1809-0.16330.09870.12130.413-0.0421-0.03070.4462-0.02210.486545.4849141.5594-45.6114
134.42440.7629-3.89435.21030.33115.56870.09160.48071.4009-0.50310.40890.6211-0.7574-0.09820.2560.70810.14080.00960.4647-0.07250.708537.8639145.3857-51.9413
145.0027-3.05450.71143.8495-1.48863.66180.13141.60210.1209-0.5534-1.0084-0.23650.25370.97550.03220.7708-0.0269-0.21831.1248-0.03560.410942.472150.0451-60.0185
155.35180.57110.89849.2183-3.33867.01040.4919-0.1484-0.14090.5419-0.9901-0.38460.56080.9050.36080.44590.04220.06130.373-0.06910.237351.3635131.6964-40.5996
165.12191.8027-0.43213.3343-1.73312.66370.33860.17340.3759-0.1089-0.5274-0.1267-0.12420.62740.16750.53420.0126-0.06180.3977-0.060.607751.4159145.4612-45.0649
173.9043-0.71970.21736.2238-6.44997.93040.5578-3.3528-0.35292.6382-0.1684-0.3671-1.1199-1.877-0.33940.8565-0.2544-0.21721.19280.08770.802846.865125.9842-28.0813
181.14970.27180.82021.4881-1.56782.5722-0.1245-0.4189-0.05160.98430.52520.217-0.0959-0.5425-0.23330.43210.05090.02370.4845-0.16770.267843.927141.9613-37.6598
194.2474-0.82912.32865.7701-3.91893.6258-0.30.1161.20780.0916-0.3348-0.721-0.8950.37240.64910.6312-0.0898-0.03810.54310.08150.814670.4031148.0426-44.891
202.4754-0.3022-0.44694.2918-0.28440.59550.19970.36790.0521-0.3649-0.46240.50220.1958-0.05460.09020.430.0216-0.06680.403-0.02070.338963.028138.4394-46.6094
215.0524-2.5153-4.06095.66923.93379.49820.02341.05431.1001-0.53930.29970.163-0.4104-1.3529-0.03990.425-0.0320.05730.44640.00340.482762.6814149.4846-53.2851
222.12740.70540.44840.5870.21210.10230.211.3103-0.2542-1.5064-0.23780.21230.5494-1.1813-0.01931.18860.073-0.32431.00960.10810.394268.0495151.3795-60.7659
236.7543.7955-4.08323.6815-1.01563.9760.2124-0.6941-0.12960.2696-0.55180.40430.36250.83730.39420.4967-0.0225-0.06550.46210.05060.45367.1289131.6271-40.5839
246.6060.1472-0.79093.9724-1.32993.4170.28860.50380.4062-0.30920.1885-0.15420.1360.0203-0.01620.4175-0.088-0.0140.4409-0.0280.682571.9071140.8435-44.4619
254.2412-0.9422.56632.36260.2314.23910.1969-0.13630.20280.7649-0.4275-0.4396-0.5878-0.04760.0790.5359-0.0006-0.05640.4479-0.12260.398568.7552142.6095-39.2676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 89 )
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 108 )
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 119 )
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 140 )
7X-RAY DIFFRACTION7chain 'A' and (resid 141 through 158 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 20 )
9X-RAY DIFFRACTION9chain 'B' and (resid 21 through 79 )
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 134 )
11X-RAY DIFFRACTION11chain 'B' and (resid 135 through 160 )
12X-RAY DIFFRACTION12chain 'C' and (resid 4 through 49 )
13X-RAY DIFFRACTION13chain 'C' and (resid 50 through 78 )
14X-RAY DIFFRACTION14chain 'C' and (resid 79 through 89 )
15X-RAY DIFFRACTION15chain 'C' and (resid 90 through 108 )
16X-RAY DIFFRACTION16chain 'C' and (resid 109 through 134 )
17X-RAY DIFFRACTION17chain 'C' and (resid 135 through 140 )
18X-RAY DIFFRACTION18chain 'C' and (resid 141 through 159 )
19X-RAY DIFFRACTION19chain 'D' and (resid 4 through 28 )
20X-RAY DIFFRACTION20chain 'D' and (resid 29 through 50 )
21X-RAY DIFFRACTION21chain 'D' and (resid 51 through 79 )
22X-RAY DIFFRACTION22chain 'D' and (resid 80 through 89 )
23X-RAY DIFFRACTION23chain 'D' and (resid 90 through 108 )
24X-RAY DIFFRACTION24chain 'D' and (resid 109 through 119 )
25X-RAY DIFFRACTION25chain 'D' and (resid 120 through 159 )

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