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- PDB-5t4y: Crystal structure of BT1762-1763 -

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Basic information

Entry
Database: PDB / ID: 5t4y
TitleCrystal structure of BT1762-1763
Components
  • SusC homolog
  • SusD homolog
KeywordsTRANSPORT PROTEIN / outer membrane protein / protein complex / TonB dependent transporter / carbohydrate binding protein
Function / homology
Function and homology information


cell outer membrane / metal ion binding
Similarity search - Function
CarboxypepD_reg-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 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor-like, beta-barrel ...CarboxypepD_reg-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 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
SusC homolog / SusD homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
Authorsvan 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
DepositionAug 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusD homolog
D: SusC homolog
B: SusD homolog
C: SusC homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,8059
Polymers362,6844
Non-polymers1225
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23350 Å2
ΔGint-140 kcal/mol
Surface area104550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.826, 152.085, 253.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SusD homolog


Mass: 65858.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
References: UniProt: Q8A6W4
#2: Protein SusC homolog


Mass: 115483.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
References: UniProt: Q8A6W3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18-20% PEG3350 50 mM Hepes pH 7.0 0.2 M NH4NO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.99→130.46 Å / Num. obs: 86975 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellHighest resolution: 2.99 Å / Rmerge(I) obs: 1.17

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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: 5T3R

5t3r


Resolution: 3.1→130.348 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.97
RfactorNum. reflection% reflection
Rfree0.2695 3941 5.09 %
Rwork0.1984 --
obs0.202 77436 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→130.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21706 0 5 0 21711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122273
X-RAY DIFFRACTIONf_angle_d1.2530221
X-RAY DIFFRACTIONf_dihedral_angle_d16.55113005
X-RAY DIFFRACTIONf_chiral_restr0.0673113
X-RAY DIFFRACTIONf_plane_restr0.0073978
LS refinement shellResolution: 3.1→3.138 Å / Rfactor Rfree: 0.467 / Rfactor Rwork: 0.385
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)
10.49860.21110.07250.5810.15720.2213-0.0527-0.2551-0.23970.486-0.0160.18250.4952-0.10250.02871.1517-0.01240.32620.70230.13040.6867-28.0075-31.29238.1671
20.460.1680.00990.62530.1390.3804-0.0762-0.27580.11830.4916-0.02640.10550.1211-0.0520.08550.67510.08750.05980.6106-0.05190.5136-16.587612.433539.4146
30.52360.22550.07241.13390.17090.7063-0.24930.1655-0.1643-0.3160.18310.04980.3820.04320.05750.708-0.13810.10570.5388-0.04650.5131-24.2687-28.8164-18.2493
40.2554-0.103-0.00090.434-0.19070.5094-0.17180.15020.1304-0.27550.09910.16690.1196-0.00730.06960.4373-0.1319-0.090.52880.08380.5716-27.720816.1304-15.3194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 552)
2X-RAY DIFFRACTION2(chain 'D' and resid 210 through 1016)
3X-RAY DIFFRACTION3(chain 'B' and resid 1 through 553)
4X-RAY DIFFRACTION4(chain 'C' and resid 210 through 1016)

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