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- PDB-5t3r: Crystal structure of BT1762-1763 -

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Basic information

Entry
Database: PDB / ID: 5t3r
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 26, 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 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4145
Polymers181,3422
Non-polymers723
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-48 kcal/mol
Surface area56030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.770, 117.330, 119.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SusD homolog


Mass: 65858.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Production host: 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Production host: 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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
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: 58.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M magnesium formate dihydrate, 0.1 M MOPS pH 7, 17% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.82→75.9 Å / Num. obs: 52316 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→75.885 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.61
RfactorNum. reflection% reflection
Rfree0.2594 2067 5.24 %
Rwork0.1972 --
obs0.2005 39461 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→75.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10854 0 3 0 10857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111132
X-RAY DIFFRACTIONf_angle_d1.27515103
X-RAY DIFFRACTIONf_dihedral_angle_d16.2836498
X-RAY DIFFRACTIONf_chiral_restr0.0721556
X-RAY DIFFRACTIONf_plane_restr0.0081987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17210.40191390.33972448X-RAY DIFFRACTION100
3.1721-3.25150.38161250.28522453X-RAY DIFFRACTION100
3.2515-3.33940.35141540.26842458X-RAY DIFFRACTION100
3.3394-3.43760.3671120.25132470X-RAY DIFFRACTION100
3.4376-3.54860.28841360.21772456X-RAY DIFFRACTION100
3.5486-3.67540.26071360.2072464X-RAY DIFFRACTION100
3.6754-3.82260.27991300.20422469X-RAY DIFFRACTION100
3.8226-3.99650.29661410.20272500X-RAY DIFFRACTION100
3.9965-4.20720.26851310.18882461X-RAY DIFFRACTION100
4.2072-4.47080.26881320.17372484X-RAY DIFFRACTION100
4.4708-4.81590.21711500.15522494X-RAY DIFFRACTION100
4.8159-5.30050.22521430.15452489X-RAY DIFFRACTION100
5.3005-6.06720.21671440.17062539X-RAY DIFFRACTION100
6.0672-7.64290.23441370.18232549X-RAY DIFFRACTION100
7.6429-75.90770.20271570.1842660X-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)
10.6292-0.22080.10441.11940.21980.57280.27170.5432-0.5175-0.4941-0.317-0.0470.0454-0.05870.02670.66530.221-0.08350.6334-0.22740.683812.8169385.578394.2618
20.9702-0.5477-0.03461.116-0.02840.0464-0.1196-0.3149-0.22060.28030.1243-0.03350.06030.01330.01560.47990.0084-0.03220.47660.0730.581418.9376389.6678139.0534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 553)
2X-RAY DIFFRACTION2(chain 'D' and resid 211 through 1016)

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