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- PDB-4r0c: Crystal structure of the Alcanivorax borkumensis YdaH transporter... -

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Basic information

Entry
Database: PDB / ID: 4r0c
TitleCrystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology
ComponentsAbgT putative transporter family
KeywordsMEMBRANE PROTEIN / Transmembrane protein
Function / homologysecondary active p-aminobenzoyl-glutamate transmembrane transporter activity / p-aminobenzoyl-glutamate transmembrane transport / p-Aminobenzoyl-glutamate transport protein AbgT / AbgT putative transporter family / membrane => GO:0016020 / AbgT putative transporter family
Function and homology information
Biological speciesAlcanivorax borkumensis SK2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.963 Å
AuthorsSu, C.-C. / Bolla, J.R. / Yu, E.W.
CitationJournal: Nat Commun / Year: 2015
Title: Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology.
Authors: Bolla, J.R. / Su, C.C. / Delmar, J.A. / Radhakrishnan, A. / Kumar, N. / Chou, T.H. / Long, F. / Rajashankar, K.R. / Yu, E.W.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AbgT putative transporter family
B: AbgT putative transporter family
C: AbgT putative transporter family
D: AbgT putative transporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,73618
Polymers206,4114
Non-polymers4,32514
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15510 Å2
ΔGint-109 kcal/mol
Surface area72200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.145, 200.984, 101.493
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AbgT putative transporter family


Mass: 51602.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcanivorax borkumensis SK2 (bacteria) / Strain: SK2 / Gene: ABO_0881, ydaH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VR69
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 4.65 Å3/Da / Density % sol: 73.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 30% PEG400, 0.05M Mg(Ac)2, 0.1M NaAc(5.0), and 3% glycerol, pH 7.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ACSD / Detector: CCD / Date: Jun 26, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 74781 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 76.18 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.96-3.091.80.543192.1
3.09-3.261.90.426196.6
3.26-3.461.90.282197.5
3.46-3.731.90.162196.5
3.73-4.120.109198.5
4.1-4.71.90.076196.9
4.7-5.9220.064198.5
5.92-501.90.04197

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.963→48.434 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 3766 5.04 %
Rwork0.2065 --
obs0.2086 74728 95.7 %
all-74728 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.86 Å2
Refinement stepCycle: LAST / Resolution: 2.963→48.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14023 0 192 58 14273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914568
X-RAY DIFFRACTIONf_angle_d1.35119950
X-RAY DIFFRACTIONf_dihedral_angle_d15.9214936
X-RAY DIFFRACTIONf_chiral_restr0.0882532
X-RAY DIFFRACTIONf_plane_restr0.0062407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.963-3.00060.32631080.28411973X-RAY DIFFRACTION72
3.0006-3.040.32211420.29442530X-RAY DIFFRACTION93
3.04-3.08170.34391410.2922558X-RAY DIFFRACTION94
3.0817-3.12570.38071150.29072680X-RAY DIFFRACTION95
3.1257-3.17230.32571450.27892625X-RAY DIFFRACTION97
3.1723-3.22190.33391370.26712614X-RAY DIFFRACTION96
3.2219-3.27470.30681340.25842682X-RAY DIFFRACTION97
3.2747-3.33120.29361370.2512636X-RAY DIFFRACTION97
3.3312-3.39170.29131270.23412694X-RAY DIFFRACTION97
3.3917-3.45690.24161340.21992628X-RAY DIFFRACTION97
3.4569-3.52750.27661470.22372592X-RAY DIFFRACTION95
3.5275-3.60420.25291380.21942620X-RAY DIFFRACTION95
3.6042-3.6880.26431390.20492650X-RAY DIFFRACTION98
3.688-3.78020.25191390.19892717X-RAY DIFFRACTION98
3.7802-3.88230.2451360.19982679X-RAY DIFFRACTION98
3.8823-3.99650.23481490.20412679X-RAY DIFFRACTION99
3.9965-4.12540.28871390.19962708X-RAY DIFFRACTION98
4.1254-4.27280.24281490.19952697X-RAY DIFFRACTION97
4.2728-4.44380.22031460.18842607X-RAY DIFFRACTION96
4.4438-4.64590.20581480.17952594X-RAY DIFFRACTION95
4.6459-4.89060.22251520.17592650X-RAY DIFFRACTION96
4.8906-5.19670.2281380.16782730X-RAY DIFFRACTION98
5.1967-5.59740.23411610.1772685X-RAY DIFFRACTION98
5.5974-6.15960.27271310.19252703X-RAY DIFFRACTION98
6.1596-7.04860.24421510.18552645X-RAY DIFFRACTION96
7.0486-8.87160.20181530.17182725X-RAY DIFFRACTION99
8.8716-48.44080.24951300.23072661X-RAY DIFFRACTION94

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