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- PDB-7t1s: Crystal structure of a bacterial sterol transporter -

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Basic information

Entry
Database: PDB / ID: 7t1s
TitleCrystal structure of a bacterial sterol transporter
ComponentsBstC
KeywordsTRANSPORT PROTEIN / sterols / transporters / methanotrophs
Function / homologyCITRIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMethylococcus capsulatus str. Texas = ATCC 19069 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsDassama, L.M.K. / Zhai, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1919153 United States
CitationJournal: Elife / Year: 2024
Title: Novel sterol binding domains in bacteria.
Authors: Zhai, L. / Bonds, A.C. / Smith, C.A. / Oo, H. / Chou, J.C. / Welander, P.V. / Dassama, L.M.K.
History
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 2.0Dec 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / citation_author / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_oper
Item: _audit_author.name / _chem_comp.formula ..._audit_author.name / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation_author.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.number_obs / _reflns.percent_possible_obs / _software.version / _struct_asym.entity_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand identity / Details: replaced two PEG with Citrate acid / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BstC
B: BstC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,59917
Polymers56,5772
Non-polymers2,02215
Water6,395355
1
A: BstC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3969
Polymers28,2891
Non-polymers1,1078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BstC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2048
Polymers28,2891
Non-polymers9157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.083, 57.257, 85.825
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein BstC


Mass: 28288.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus str. Texas = ATCC 19069 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3500, ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97896, 0.91837, 0.97930
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 17, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.918371
30.97931
ReflectionResolution: 1.91→28.63 Å / Num. obs: 80757 / % possible obs: 99.91 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.59 Å2 / CC1/2: 0.994 / Net I/σ(I): 11.09
Reflection shellResolution: 1.91→1.978 Å / Num. unique obs: 4084 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→28.63 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 3904 4.85 %
Rwork0.1723 --
obs0.174 80436 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 135 355 4036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153739
X-RAY DIFFRACTIONf_angle_d1.6145031
X-RAY DIFFRACTIONf_dihedral_angle_d18.656565
X-RAY DIFFRACTIONf_chiral_restr0.063507
X-RAY DIFFRACTIONf_plane_restr0.021682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.26761330.25262614X-RAY DIFFRACTION97
1.93-1.960.2671400.23282756X-RAY DIFFRACTION99
1.96-1.980.26811410.22682726X-RAY DIFFRACTION99
1.98-2.010.24831390.21942658X-RAY DIFFRACTION99
2.01-2.040.24071440.20372850X-RAY DIFFRACTION99
2.04-2.070.23741320.19642663X-RAY DIFFRACTION99
2.07-2.10.21541400.18192759X-RAY DIFFRACTION99
2.1-2.130.21641370.17192685X-RAY DIFFRACTION100
2.13-2.170.19111360.16642706X-RAY DIFFRACTION100
2.17-2.210.22441400.16442788X-RAY DIFFRACTION100
2.21-2.250.18691410.15912713X-RAY DIFFRACTION99
2.25-2.30.19371430.15452795X-RAY DIFFRACTION100
2.3-2.350.18411380.15682695X-RAY DIFFRACTION99
2.35-2.40.19021350.15492768X-RAY DIFFRACTION100
2.4-2.460.22531420.15732685X-RAY DIFFRACTION100
2.46-2.530.25231410.15672773X-RAY DIFFRACTION100
2.53-2.610.20991400.15782735X-RAY DIFFRACTION100
2.61-2.690.19271400.15612710X-RAY DIFFRACTION100
2.69-2.790.20751390.16582767X-RAY DIFFRACTION100
2.79-2.90.18311400.15682743X-RAY DIFFRACTION100
2.9-3.030.21981420.17652748X-RAY DIFFRACTION100
3.03-3.190.23521400.17842762X-RAY DIFFRACTION100
3.19-3.390.20291370.17482707X-RAY DIFFRACTION100
3.39-3.650.22491420.16062752X-RAY DIFFRACTION100
3.65-4.010.14791360.15282731X-RAY DIFFRACTION100
4.01-4.590.17091410.14972759X-RAY DIFFRACTION100
4.59-5.780.1681450.18082747X-RAY DIFFRACTION100
5.78-100.24911400.20792737X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.9014 Å / Origin y: 35.0301 Å / Origin z: 19.6085 Å
111213212223313233
T0.0992 Å2-0.0105 Å20.0041 Å2-0.1011 Å2-0.0173 Å2--0.0992 Å2
L0.1412 °2-0.127 °20.1502 °2-0.3717 °2-0.267 °2--0.4321 °2
S0.0071 Å °-0.0139 Å °0.0058 Å °0.0281 Å °0.0016 Å °0.008 Å °0.0357 Å °-0.0004 Å °-0.0089 Å °
Refinement TLS groupSelection details: all

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