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- PDB-4dve: Crystal structure at 2.1 A of the S-component for biotin from an ... -

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Basic information

Entry
Database: PDB / ID: 4dve
TitleCrystal structure at 2.1 A of the S-component for biotin from an ECF-type ABC transporter
ComponentsBiotin transporter BioY
KeywordsTRANSPORT PROTEIN / ECF-transport / Ligand-binding domain / biotin binding / Membrane
Function / homology
Function and homology information


biotin transmembrane transporter activity / plasma membrane
Similarity search - Function
BioY protein / BioY family / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BIOTIN / Biotin transporter BioY
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsBerntsson, R.P.-A. / ter Beek, J. / Majsnerowska, M. / Duurkens, R. / Puri, P. / Poolman, B. / Slotboom, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural divergence of paralogous S components from ECF-type ABC transporters.
Authors: Berntsson, R.P. / Ter Beek, J. / Majsnerowska, M. / Duurkens, R.H. / Puri, P. / Poolman, B. / Slotboom, D.J.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biotin transporter BioY
B: Biotin transporter BioY
C: Biotin transporter BioY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,42812
Polymers65,8573
Non-polymers2,5719
Water2,090116
1
A: Biotin transporter BioY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1165
Polymers21,9521
Non-polymers1,1634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Biotin transporter BioY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8094
Polymers21,9521
Non-polymers8573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Biotin transporter BioY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5033
Polymers21,9521
Non-polymers5512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Biotin transporter BioY
B: Biotin transporter BioY
C: Biotin transporter BioY
hetero molecules

A: Biotin transporter BioY
B: Biotin transporter BioY
C: Biotin transporter BioY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,85724
Polymers131,7146
Non-polymers5,14318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area17980 Å2
ΔGint-38 kcal/mol
Surface area49230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.825, 57.384, 166.865
Angle α, β, γ (deg.)90.00, 91.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-202-

BNG

21B-202-

BNG

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 1 - 188 / Label seq-ID: 11 - 198

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Biotin transporter BioY / Biotin ECF transporter S component BioY


Mass: 21952.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Strain: MG1363 / Gene: bioY, llmg_1964 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: A2RMJ9
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05-0.2 mM CaCl2, 45-50% PEG400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97935 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.09→48.36 Å / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.97 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.09-2.220.4382.51580071448490.7
2.22-2.370.3024.73850481481599.8
2.37-2.560.1957.31809911385599.9
2.56-2.810.13310.63755141280399.9
2.81-3.140.08716.29673431152699.9
3.14-3.620.0624.14587931012699.9
3.62-4.430.04434.3748195864799.8
4.43-6.230.04137.7436837659799.9
6.230.03441.6621077372799.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.09→48.36 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2049 / WRfactor Rwork: 0.1869 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9118 / SU B: 5.159 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1592 / SU Rfree: 0.1357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 2488 5 %RANDOM
Rwork0.1855 ---
obs0.1864 49743 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 119.41 Å2 / Biso mean: 47.026 Å2 / Biso min: 25.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20.28 Å2
2--2.93 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.09→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4329 0 174 116 4619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024624
X-RAY DIFFRACTIONr_bond_other_d0.0010.023203
X-RAY DIFFRACTIONr_angle_refined_deg1.5672.0286263
X-RAY DIFFRACTIONr_angle_other_deg1.32237863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2065565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40422.391138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96715691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0341515
X-RAY DIFFRACTIONr_chiral_restr0.1580.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02979
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1086MEDIUM POSITIONAL0.190.5
B1086MEDIUM POSITIONAL0.170.5
C1086MEDIUM POSITIONAL0.180.5
A1347LOOSE POSITIONAL0.665
B1347LOOSE POSITIONAL0.65
C1347LOOSE POSITIONAL0.665
A1086MEDIUM THERMAL3.032
B1086MEDIUM THERMAL3.022
C1086MEDIUM THERMAL4.72
A1347LOOSE THERMAL3.8410
B1347LOOSE THERMAL3.5410
C1347LOOSE THERMAL5.510
LS refinement shellResolution: 2.094→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 154 -
Rwork0.211 2933 -
all-3087 -
obs--85.35 %
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)
13.4916-1.36840.35351.4983-0.39351.8702-0.0438-0.1011-0.00850.04190.05190.0548-0.1648-0.0207-0.00810.04660.04530.0070.06280.01940.068734.9617-43.435969.8979
23.24761.5188-0.84841.568-0.25721.84950.0435-0.2032-0.11010.0541-0.0728-0.06450.10350.10590.02930.0655-0.0351-0.00210.04020.01690.068136.7855-15.933414.1918
31.84540.27150.36943.4998-1.93924.07340.00070.1404-0.00060.06870.12450.15240.0604-0.068-0.12520.0510.00230.0010.05080.03030.024827.8339-29.30941.2024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 188
2X-RAY DIFFRACTION2B0 - 188
3X-RAY DIFFRACTION3C1 - 188

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