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- PDB-5fq6: Crystal structure of the SusCD complex BT2261-2264 from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 5fq6
TitleCrystal structure of the SusCD complex BT2261-2264 from Bacteroides thetaiotaomicron
Components
  • BT_2261
  • PUTATIVE LIPOPROTEIN
  • SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
  • UNCHARACTERIZED PROTEIN
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE NUTRIENT IMPORTER SUSCD COMPLEX
Function / homology
Function and homology information


cell outer membrane / metal ion binding
Similarity search - Function
Lipocalin - #220 / Lipid-binding, putative / Lipid-binding superfamily / Lipid-binding putative hydrolase / SusD-like 2 / Starch-binding associating with outer membrane / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / TonB dependent receptor ...Lipocalin - #220 / Lipid-binding, putative / Lipid-binding superfamily / Lipid-binding putative hydrolase / SusD-like 2 / Starch-binding associating with outer membrane / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Lipocalin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
3-decanoyloxypropyl decanoate / Outer membrane protein Omp121 / Lipoprotein / Lipid-binding hydrolase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGlenwright, A.J. / Pothula, K.R. / Chorev, D.S. / Basle, A. / Robinson, C.V. / Kleinekathoefer, U. / Bolam, D.N. / van den Berg, B.
CitationJournal: Nature / Year: 2017
Title: Structural basis for nutrient acquisition by dominant members of the human gut microbiota.
Authors: Glenwright, A.J. / Pothula, K.R. / Bhamidimarri, S.P. / Chorev, D.S. / Basle, A. / Firbank, S.J. / Zheng, H. / Robinson, C.V. / Winterhalter, M. / Kleinekathofer, U. / Bolam, D.N. / van den Berg, B.
History
DepositionDec 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Feb 1, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / 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 / _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.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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "ID" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "MD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "NA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE LIPOPROTEIN
B: SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
C: PUTATIVE LIPOPROTEIN
D: SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
E: UNCHARACTERIZED PROTEIN
F: UNCHARACTERIZED PROTEIN
G: BT_2261
H: PUTATIVE LIPOPROTEIN
I: SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
J: UNCHARACTERIZED PROTEIN
K: BT_2261
L: PUTATIVE LIPOPROTEIN
M: SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
N: UNCHARACTERIZED PROTEIN
O: BT_2261
P: BT_2261
hetero molecules


Theoretical massNumber of molelcules
Total (without water)718,26128
Polymers716,47016
Non-polymers1,79112
Water0
1
C: PUTATIVE LIPOPROTEIN
D: SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
E: UNCHARACTERIZED PROTEIN
G: BT_2261
L: PUTATIVE LIPOPROTEIN
M: SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
N: UNCHARACTERIZED PROTEIN
O: BT_2261
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,13014
Polymers358,2358
Non-polymers8956
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28600 Å2
ΔGint-167.6 kcal/mol
Surface area108950 Å2
MethodPISA
2
A: PUTATIVE LIPOPROTEIN
B: SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
F: UNCHARACTERIZED PROTEIN
H: PUTATIVE LIPOPROTEIN
I: SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN
J: UNCHARACTERIZED PROTEIN
K: BT_2261
P: BT_2261
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,13014
Polymers358,2358
Non-polymers8956
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28460 Å2
ΔGint-159.2 kcal/mol
Surface area108690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.027, 91.941, 261.219
Angle α, β, γ (deg.)90.00, 98.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 12 molecules ACHLBDIMEFJN

#1: Protein
PUTATIVE LIPOPROTEIN /


Mass: 53145.875 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H6
#2: Protein
SUSC/RAGA FAMILY TONB-LINKED OUTER MEMBRANE PROTEIN


Mass: 108954.195 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: TONB DEPENDENT TRANSPORTER / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H5
#3: Protein
UNCHARACTERIZED PROTEIN


Mass: 16428.965 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H8

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Protein/peptide , 1 types, 4 molecules GKOP

#4: Protein/peptide
BT_2261


Mass: 588.533 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria)

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Non-polymers , 3 types, 12 molecules

#5: Chemical
ChemComp-KR0 / 3-decanoyloxypropyl decanoate


Mass: 384.593 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H44O4
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.7 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growDetails: 0.2 M MAGNESIUM FORMATE DIHYDRATE 0.05 M TRIS PH 8 18-22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→48.8 Å / Num. obs: 256052 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 5FQ4 AND 5FQ3

5fq4

5fq3


Resolution: 2.8→48.799 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 31.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 10251 4 %
Rwork0.1982 --
obs0.2005 255319 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49146 0 116 0 49262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00850457
X-RAY DIFFRACTIONf_angle_d1.0868497
X-RAY DIFFRACTIONf_dihedral_angle_d15.60229507
X-RAY DIFFRACTIONf_chiral_restr0.0567255
X-RAY DIFFRACTIONf_plane_restr0.0079011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.37183510.31498002X-RAY DIFFRACTION99
2.8318-2.86510.36633350.30248138X-RAY DIFFRACTION99
2.8651-2.90010.39393640.30638051X-RAY DIFFRACTION99
2.9001-2.93680.36523220.29088082X-RAY DIFFRACTION99
2.9368-2.97540.35233500.28178143X-RAY DIFFRACTION99
2.9754-3.01620.39073190.27198032X-RAY DIFFRACTION99
3.0162-3.05930.32493300.26778161X-RAY DIFFRACTION99
3.0593-3.10490.34593750.24848029X-RAY DIFFRACTION99
3.1049-3.15340.30613510.24398138X-RAY DIFFRACTION99
3.1534-3.20510.33823170.24568145X-RAY DIFFRACTION99
3.2051-3.26040.32223330.23798130X-RAY DIFFRACTION99
3.2604-3.31960.32693170.23588075X-RAY DIFFRACTION99
3.3196-3.38350.26233540.22048191X-RAY DIFFRACTION99
3.3835-3.45250.27643110.21758116X-RAY DIFFRACTION99
3.4525-3.52760.30243290.22348232X-RAY DIFFRACTION99
3.5276-3.60960.2663580.19338076X-RAY DIFFRACTION99
3.6096-3.69980.23373520.19098202X-RAY DIFFRACTION99
3.6998-3.79980.26193250.1868179X-RAY DIFFRACTION100
3.7998-3.91160.24663640.18498095X-RAY DIFFRACTION99
3.9116-4.03780.24623350.17978201X-RAY DIFFRACTION99
4.0378-4.1820.24653530.17378231X-RAY DIFFRACTION99
4.182-4.34940.21333300.15668197X-RAY DIFFRACTION100
4.3494-4.54720.17483540.14748190X-RAY DIFFRACTION100
4.5472-4.78670.17633340.13728218X-RAY DIFFRACTION100
4.7867-5.08630.1843450.14118262X-RAY DIFFRACTION100
5.0863-5.47860.21993430.16378251X-RAY DIFFRACTION100
5.4786-6.0290.22783620.17918274X-RAY DIFFRACTION100
6.029-6.89930.21473660.17858283X-RAY DIFFRACTION100
6.8993-8.68440.22173230.17058381X-RAY DIFFRACTION100
8.6844-48.80640.21213490.20668363X-RAY DIFFRACTION97
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)
11.3133-0.08180.24330.6148-0.01980.84470.0407-0.2517-0.37730.06430.03910.27890.1983-0.5358-0.06410.4059-0.162-0.03120.70860.12640.5054-87.05-26.5385-89.6186
21.209-0.15540.46460.2706-0.08920.4295-0.0170.5303-0.0431-0.14590.0225-0.03-0.01630.1769-0.00440.4131-0.0653-0.00140.59990.00380.3067-51.3782-11.879-112.3548
30.6936-0.03910.20570.97840.01910.9129-0.14540.10010.1184-0.26250.00060.3548-0.241-0.01770.12770.63150.0836-0.21820.92740.15540.6625-101.539310.4441-122.8767
43.1554-0.92680.67032.0395-2.01532.01250.34070.4005-0.4024-0.3092-0.37740.23330.1760.0671-0.03280.4777-0.1567-0.01750.3956-0.03840.4023-73.8096-10.854-102.6436
51.25760.20610.25180.41180.04960.7286-0.0460.3376-0.3327-0.1022-0.0027-0.14410.20040.42290.03730.4190.13410.05830.506-0.11510.4587-116.5464-27.6602-40.8369
61.17590.16260.20660.0968-0.04130.4576-0.059-0.2492-0.00280.02560.03750.019-0.0097-0.02690.02620.45220.04240.01970.2145-0.02770.3928-152.1797-14.355-16.9214
70.82030.02090.08430.98-0.01730.9174-0.0792-0.19730.17270.17710.0082-0.3203-0.18330.23450.07310.4501-0.0856-0.09660.6663-0.08710.4716-101.78567.5016-5.8139
81.8981-1.01550.08930.58380.28842.90140.157-0.3026-0.2960.1827-0.2528-0.14110.1397-0.0912-0.02970.51580.15870.05840.3164-0.1180.4715-129.7584-12.7998-26.9571
91.2148-0.2630.1790.6446-0.33250.7995-0.1954-0.7427-0.09980.18880.25620.2324-0.0257-0.5114-0.03710.44280.12280.06761.01970.13640.4252-59.8413-13.0295-45.4896
101.0548-0.11780.3850.2501-0.05140.5656-0.0603-0.04-0.08930.00410.0658-0.00340.01350.0039-0.0040.4296-0.03070.02230.25320.06460.3809-22.647-17.9189-70.398
110.52260.1474-0.31770.6635-0.14451.1082-0.0796-0.5656-0.32420.22340.0608-0.0860.22390.10010.09210.6144-0.00790.0141.12050.49920.7074-28.3547-47.6896-23.135
122.8899-0.7679-0.06720.20420.03323.94570.2239-0.078-0.11850.1429-0.405-0.5922-0.06680.12690.15790.4687-0.03730.0190.40280.16670.3711-40.104-24.2875-53.9946
130.95750.25790.24030.5250.35620.8817-0.2660.98420.0018-0.21140.2876-0.2188-0.12410.5866-0.03190.5033-0.26360.08631.448-0.10240.4452-144.074-11.536-83.9479
140.96950.03180.33030.23110.06630.5935-0.10040.2939-0.04120.00370.08180.02070.03540.04440.02170.4533-0.02320.03130.2561-0.07350.4187-181.0912-18.0442-59.1259
150.5122-0.17220.05340.74490.15260.7237-0.07520.4866-0.2802-0.26690.05740.09920.2344-0.10440.08310.6594-0.09960.01561.4406-0.55950.6189-175.6394-44.8052-108.1882
163.72130.91560.10510.3824-0.84694.90410.29770.2621-0.1795-0.1541-0.58240.85820.0474-0.31380.32130.4091-0.1170.04180.4205-0.05790.3945-163.6241-23.1595-75.8234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 0 THROUGH 480)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 37 THROUGH 984)
3X-RAY DIFFRACTION3(CHAIN 'F' AND RESID 3 THROUGH 148)
4X-RAY DIFFRACTION4(CHAIN 'P' AND RESID 1 THROUGH 10)
5X-RAY DIFFRACTION5(CHAIN 'C' AND RESID 0 THROUGH 480)
6X-RAY DIFFRACTION6(CHAIN 'D' AND RESID 37 THROUGH 984)
7X-RAY DIFFRACTION7(CHAIN 'E' AND RESID 3 THROUGH 148)
8X-RAY DIFFRACTION8(CHAIN 'G' AND RESID 1 THROUGH 10)
9X-RAY DIFFRACTION9(CHAIN 'H' AND RESID 0 THROUGH 480)
10X-RAY DIFFRACTION10(CHAIN 'I' AND RESID 38 THROUGH 984)
11X-RAY DIFFRACTION11(CHAIN 'J' AND RESID 3 THROUGH 148)
12X-RAY DIFFRACTION12(CHAIN 'K' AND RESID 1 THROUGH 10)
13X-RAY DIFFRACTION13(CHAIN 'L' AND RESID 0 THROUGH 480)
14X-RAY DIFFRACTION14(CHAIN 'M' AND RESID 37 THROUGH 984)
15X-RAY DIFFRACTION15(CHAIN 'N' AND RESID 3 THROUGH 148)
16X-RAY DIFFRACTION16(CHAIN 'O' AND RESID 1 THROUGH 10)

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