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- PDB-3zuy: Crystal structure of a bacterial homologue of the bile acid sodiu... -

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Basic information

Entry
Database: PDB / ID: 3zuy
TitleCrystal structure of a bacterial homologue of the bile acid sodium symporter ASBT.
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Bile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / TAUROCHOLIC ACID / Transporter
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHu, N.-J. / Iwata, S. / Cameron, A.D. / Drew, D.
CitationJournal: Nature / Year: 2011
Title: Crystal Structure of a Bacterial Homologue of the Bile Acid Sodium Symporter Asbt.
Authors: Hu, N.-J. / Iwata, S. / Cameron, A.D. / Drew, D.
History
DepositionJul 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references / Structure summary
Revision 1.2May 31, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,59412
Polymers33,9021
Non-polymers3,69211
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint4 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.350, 73.350, 162.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transporter


Mass: 33901.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0705 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9K0A9

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-TCH / TAUROCHOLIC ACID


Mass: 515.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H45NO7S
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsLEU87CYS, ILE138THR, THR256ALA MUTATIONS OBSERVED PREVIOUSLY IN PDB ENTRY 3ZUX HAVE BEEN CORRECTED ...LEU87CYS, ILE138THR, THR256ALA MUTATIONS OBSERVED PREVIOUSLY IN PDB ENTRY 3ZUX HAVE BEEN CORRECTED IN THIS WILDTYPE STRUCTURE.

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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: 3.34 Å3/Da / Density % sol: 63.17 % / Description: NONE
Crystal growpH: 4.5
Details: 50 MM SODIUM CITRATE PH 4.5, 70 MM NACL, AND 22-24% PEG400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9778
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 28, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.2→24.4 Å / Num. obs: 22917 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 39.94 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALEPACKdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZUX

3zux


Resolution: 2.2→24.42 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9094 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA TCH LDA PTY. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2290. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA TCH LDA PTY. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2290. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=191. NUMBER TREATED BY BAD NON- BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 1158 5.05 %RANDOM
Rwork0.2116 ---
obs0.2132 22915 --
Displacement parametersBiso mean: 64.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.4113 Å20 Å20 Å2
2--2.4113 Å20 Å2
3----4.8226 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 193 26 2483
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012508HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043410HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d892SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes342HARMONIC5
X-RAY DIFFRACTIONt_it2508HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion17.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion327SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3075SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2633 150 5.4 %
Rwork0.2233 2627 -
all0.2254 2777 -
Refinement TLS params.Method: refined / Origin x: 18.3243 Å / Origin y: 69.599 Å / Origin z: 80.2044 Å
111213212223313233
T-0.2668 Å2-0.0241 Å20.0156 Å2-0.296 Å2-0.0173 Å2---0.2914 Å2
L2.8953 °20.2966 °20.0112 °2-1.0969 °20.342 °2--3.0232 °2
S-0.0375 Å °0.5461 Å °0.1327 Å °0.0035 Å °0.2568 Å °-0.0319 Å °-0.1032 Å °0.3481 Å °-0.2193 Å °
Refinement TLS groupSelection details: { A|2-1320 }

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