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- PDB-5fq4: Crystal structure of the lipoprotein BT2263 from Bacteroides thet... -

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Basic information

Entry
Database: PDB / ID: 5fq4
TitleCrystal structure of the lipoprotein BT2263 from Bacteroides thetaiotaomicron
ComponentsPUTATIVE LIPOPROTEIN
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE LIPOPROTEIN
Function / homology
Function and homology information


SusD-like 2 / Starch-binding associating with outer membrane / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 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_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_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_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE LIPOPROTEIN
B: PUTATIVE LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6024
Polymers106,5222
Non-polymers802
Water15,781876
1
A: PUTATIVE LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3012
Polymers53,2611
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3012
Polymers53,2611
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.757, 80.025, 120.047
Angle α, β, γ (deg.)90.00, 100.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PUTATIVE LIPOPROTEIN / BT_2263


Mass: 53261.004 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 20-498
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL CYSTEINE RESIDUE REMOVED
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A5H6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM ACETATE TRIHYDRATE 0.1 M TRIS PH 8.5 30% V/V PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.9→47.75 Å / Num. obs: 81475 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 23.39 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q69

4q69


Resolution: 1.9→47.535 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 2030 2.5 %
Rwork0.1583 --
obs0.1593 80356 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7182 0 2 876 8060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077381
X-RAY DIFFRACTIONf_angle_d0.80210028
X-RAY DIFFRACTIONf_dihedral_angle_d11.7324332
X-RAY DIFFRACTIONf_chiral_restr0.0471082
X-RAY DIFFRACTIONf_plane_restr0.0051308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.33661190.29255569X-RAY DIFFRACTION100
1.9475-2.00020.25251300.23365586X-RAY DIFFRACTION100
2.0002-2.0590.271520.2215511X-RAY DIFFRACTION99
2.059-2.12550.22191510.19925582X-RAY DIFFRACTION100
2.1255-2.20150.26091320.18045597X-RAY DIFFRACTION100
2.2015-2.28960.23121350.18065582X-RAY DIFFRACTION100
2.2896-2.39380.20881570.16355549X-RAY DIFFRACTION100
2.3938-2.520.19761670.16075557X-RAY DIFFRACTION100
2.52-2.67790.24911480.16235579X-RAY DIFFRACTION100
2.6779-2.88460.21811680.1595609X-RAY DIFFRACTION100
2.8846-3.17480.2051620.15345560X-RAY DIFFRACTION100
3.1748-3.63410.19481530.1395628X-RAY DIFFRACTION100
3.6341-4.5780.14081210.11975675X-RAY DIFFRACTION100
4.578-47.55030.1421350.13895742X-RAY DIFFRACTION100
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)
11.59010.2939-0.5632.274-0.89151.4863-0.0284-0.3403-0.18260.2515-0.1165-0.151-0.0350.25710.14540.1369-0.0054-0.00080.22940.02210.1565-13.52456.0919174.0643
21.93230.9081-0.77563.1555-0.9961.1521-0.1372-0.1796-0.5558-0.1188-0.1988-0.64430.2560.28960.28790.22280.08320.09040.27990.11660.4259-4.522-5.4232167.4527
30.74840.09760.14711.7217-0.42160.6179-0.2119-0.0344-0.3337-0.10930.08680.01590.4267-0.00550.150.2632-0.00190.11040.1552-0.01150.3637-21.0056-9.4126168.4627
42.18850.0944-0.85832.6437-0.13031.1438-0.39930.0246-0.44980.0783-0.00240.26370.5499-0.0640.37940.2329-0.00580.01220.14630.02290.2465-22.5066-2.8188165.425
51.76720.3598-0.952.5534-1.41451.76680.21750.04460.36150.31780.09560.2358-0.3882-0.1304-0.28010.17740.01770.04280.1773-0.00220.2221-27.606823.0306167.4369
61.66880.2256-0.99351.4699-0.73911.3602-0.11090.2124-0.0851-0.21290.05460.07950.1472-0.16180.03570.1493-0.0325-0.00840.1769-0.02190.1352-20.931310.4029156.3791
70.82450.589-0.22012.3959-0.28291.47070.048-0.05950.0049-0.0554-0.0875-0.2335-0.22480.19510.03360.14480.00420.00010.17830.02340.143410.517836.6609137.4948
81.8710.9844-2.19111.2209-1.13694.30050.1225-0.03670.1533-0.00510.01780.209-0.3672-0.0271-0.17470.27410.0566-0.01320.2080.0060.217-2.674944.1788136.6553
90.97960.1854-0.0423.149-0.59593.02250.18030.16830.1906-0.3617-0.02370.029-0.5376-0.1239-0.18690.2171-0.0119-0.01270.14670.03160.2216-0.621340.7347130.8357
100.75510.9681-0.44323.0351-0.59282.1471-0.19650.1508-0.226-0.57320.0513-0.20990.4995-0.1230.14240.3165-0.01210.03020.2092-0.0220.1768-0.790414.8458126.0553
110.81170.2423-0.31141.3736-0.29771.4913-0.02010.09780.0493-0.13910.04750.2607-0.0132-0.3155-0.00940.13210.0105-0.01760.1980.02070.171-8.34427.4296136.5606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 18 THROUGH 119 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 120 THROUGH 158 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 159 THROUGH 195 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 196 THROUGH 234 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 235 THROUGH 321 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 322 THROUGH 480 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 18 THROUGH 174 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 175 THROUGH 196 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 197 THROUGH 234 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 235 THROUGH 321 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 322 THROUGH 480 )

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