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- PDB-5fq8: Crystal structure of the SusCD complex BT2261-2264 from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 5fq8
TitleCrystal structure of the SusCD complex BT2261-2264 from Bacteroides thetaiotaomicron
Components
  • (UNCHARACTERISED PROTEIN, BOUND ...) x 2
  • BT_2262 (UNCHARACTERISED LIPOPROTEIN)
  • OUTER MEMBRANE PROTEIN OMP121
  • PUTATIVE LIPOPROTEIN
  • 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
Domain of unknown function DUF5012 / BT_2262-like, C-terminal domain / Lipocalin - #220 / Lipid-binding, putative / Lipid-binding superfamily / Lipid-binding putative hydrolase / SusD-like 2 / Starch-binding associating with outer membrane / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain ...Domain of unknown function DUF5012 / BT_2262-like, C-terminal domain / Lipocalin - #220 / Lipid-binding, putative / Lipid-binding superfamily / Lipid-binding putative hydrolase / SusD-like 2 / Starch-binding associating with outer membrane / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / 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 (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB dependent receptor-like, beta-barrel / 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 / Immunoglobulin-like fold / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
3-decanoyloxypropyl decanoate / Outer membrane protein Omp121 / Lipoprotein / DUF5012 domain-containing protein / Lipid-binding hydrolase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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_conn_type / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE LIPOPROTEIN
B: OUTER MEMBRANE PROTEIN OMP121
C: PUTATIVE LIPOPROTEIN
D: OUTER MEMBRANE PROTEIN OMP121
E: UNCHARACTERIZED PROTEIN
F: UNCHARACTERIZED PROTEIN
G: BT_2262 (UNCHARACTERISED LIPOPROTEIN)
P: UNCHARACTERISED PROTEIN, BOUND PEPTIDE
Q: UNCHARACTERISED PROTEIN, BOUND PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,83023
Polymers381,5789
Non-polymers2,25214
Water16,718928
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36270 Å2
ΔGint-202.4 kcal/mol
Surface area116580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.110, 122.743, 122.830
Angle α, β, γ (deg.)111.41, 98.33, 98.51
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 7 molecules ACBDEFG

#1: Protein PUTATIVE LIPOPROTEIN


Mass: 53145.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H6
#2: Protein OUTER MEMBRANE PROTEIN OMP121


Mass: 108954.195 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H8
#4: Protein BT_2262 (UNCHARACTERISED LIPOPROTEIN)


Mass: 23399.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H7

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UNCHARACTERISED PROTEIN, BOUND ... , 2 types, 2 molecules PQ

#5: Protein/peptide UNCHARACTERISED PROTEIN, BOUND PEPTIDE


Mass: 588.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria)
#6: Protein/peptide UNCHARACTERISED PROTEIN, BOUND PEPTIDE


Mass: 531.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria)

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Non-polymers , 5 types, 942 molecules

#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-KR0 / 3-decanoyloxypropyl decanoate


Mass: 384.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H44O4
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#10: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIDENTITY OF PEPTIDE LIGAND UNKNOWN. ASSIGNED SEQUENCE FITS REASONABLY WELL IN DENSITY. LIKELY AN ...IDENTITY OF PEPTIDE LIGAND UNKNOWN. ASSIGNED SEQUENCE FITS REASONABLY WELL IN DENSITY. LIKELY AN ENSEMBLE OF BOUND PEPTIDES IS PRESENT

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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: 3.1 Å3/Da / Density % sol: 60 % / 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: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→66.95 Å / Num. obs: 125711 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.8
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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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, 3H3I, 1FEP

5fq4

3h3i

1fep


Resolution: 2.75→52.933 Å / SU ML: 0.39 / σ(F): 1.96 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 6248 5 %
Rwork0.2052 --
obs0.2079 125658 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→52.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26190 0 97 928 27215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01426945
X-RAY DIFFRACTIONf_angle_d0.94236506
X-RAY DIFFRACTIONf_dihedral_angle_d12.8715733
X-RAY DIFFRACTIONf_chiral_restr0.0543871
X-RAY DIFFRACTIONf_plane_restr0.0064790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.78120.35112100.29454050X-RAY DIFFRACTION100
2.7812-2.8140.35242200.28053886X-RAY DIFFRACTION100
2.814-2.84830.34241960.27534072X-RAY DIFFRACTION100
2.8483-2.88430.3222220.27853930X-RAY DIFFRACTION100
2.8843-2.92230.31642530.26943922X-RAY DIFFRACTION100
2.9223-2.96230.33662340.2693940X-RAY DIFFRACTION100
2.9623-3.00460.34312350.26183970X-RAY DIFFRACTION100
3.0046-3.04950.34881990.25423955X-RAY DIFFRACTION100
3.0495-3.09710.34431680.25144044X-RAY DIFFRACTION100
3.0971-3.14790.33442160.25724031X-RAY DIFFRACTION100
3.1479-3.20220.29981990.24613924X-RAY DIFFRACTION100
3.2022-3.26040.34022000.24633953X-RAY DIFFRACTION100
3.2604-3.32310.30172050.23944067X-RAY DIFFRACTION100
3.3231-3.39090.29491690.23414020X-RAY DIFFRACTION100
3.3909-3.46460.30912220.23323908X-RAY DIFFRACTION100
3.4646-3.54520.30172380.2133996X-RAY DIFFRACTION100
3.5452-3.63380.27581910.20593990X-RAY DIFFRACTION100
3.6338-3.73210.26031900.20854003X-RAY DIFFRACTION100
3.7321-3.84190.2241950.19184035X-RAY DIFFRACTION100
3.8419-3.96580.27421890.20783955X-RAY DIFFRACTION100
3.9658-4.10750.21931820.18333975X-RAY DIFFRACTION100
4.1075-4.27190.22441920.17043982X-RAY DIFFRACTION100
4.2719-4.46620.18221900.15674031X-RAY DIFFRACTION100
4.4662-4.70160.19992110.15123971X-RAY DIFFRACTION100
4.7016-4.99590.19072260.14783956X-RAY DIFFRACTION100
4.9959-5.38130.19872400.15783968X-RAY DIFFRACTION100
5.3813-5.92220.22182020.17683966X-RAY DIFFRACTION100
5.9222-6.77770.21552310.17263974X-RAY DIFFRACTION100
6.7777-8.53330.18732160.16123984X-RAY DIFFRACTION100
8.5333-52.94230.22072070.18133952X-RAY DIFFRACTION99
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)
10.7944-0.2913-0.45070.74110.25131.24730.0125-0.21490.25070.19750.0992-0.1312-0.26220.209-0.10450.5112-0.015-0.01570.3378-0.05270.315659.665393.263466.9882
20.66850.1883-0.0470.6126-0.12790.63620.0372-0.03430.0815-0.0169-0.0164-0.0156-0.1359-0.0213-0.01950.43030.07020.03810.22690.01590.212852.1206107.35816.0245
30.39230.0205-0.0850.44940.03530.4120.00820.0609-0.0431-0.0966-0.03510.02380.0956-0.04670.02390.43380.05470.01220.24310.0010.220854.011563.54616.6845
40.3479-0.1773-0.16810.32650.19430.6789-0.0483-0.0082-0.10420.0628-0.00750.06180.2192-0.02040.04690.53750.03910.04370.25590.02420.274342.4753.53155.2835
51.1930.48620.76360.5838-0.23992.3105-0.0499-0.09180.04740.1396-0.07610.07910.0124-0.15710.13720.5070.06520.13080.30640.02770.309518.045782.715596.5899
62.1896-0.43780.62181.59740.00872.4667-0.00150.54190.1336-0.2671-0.0518-0.3586-0.15550.36240.05410.4542-0.00960.10310.44240.00390.295489.243198.688-18.9599
72.51371.45950.70722.8563-0.04071.3732-0.2037-0.21670.94530.0388-0.19690.2731-0.5641-0.28850.36590.61020.0644-0.05120.5419-0.08430.657498.5479116.27713.7505
84.70090.2514-2.31883.11.07752.6618-0.06940.75371.3396-0.66490.01770.6272-0.2319-0.22150.04050.53720.1083-0.03760.19080.05410.394362.332986.66458.5834
90.4870.5383-0.11621.2738-1.51262.8503-0.1004-0.4211-0.24380.21030.1810.1507-0.16340.1234-0.06850.3555-0.02840.0570.37020.08530.251141.336976.912764.7443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'C' AND RESID 0 THROUGH 479)
2X-RAY DIFFRACTION2(CHAIN 'A' AND RESID 0 THROUGH 480)
3X-RAY DIFFRACTION3(CHAIN 'B' AND RESID 37 THROUGH 984)
4X-RAY DIFFRACTION4(CHAIN 'D' AND RESID 37 THROUGH 984)
5X-RAY DIFFRACTION5(CHAIN 'E' AND RESID 4 THROUGH 148)
6X-RAY DIFFRACTION6(CHAIN 'F' AND RESID 3 THROUGH 148)
7X-RAY DIFFRACTION7(CHAIN 'G' AND RESID 1 THROUGH 212)
8X-RAY DIFFRACTION8(CHAIN 'P' AND RESID 1 THROUGH 10)
9X-RAY DIFFRACTION9(CHAIN 'Q' AND RESID 1 THROUGH 9)

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