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- PDB-3rlb: Crystal structure at 2.0 A of the S-component for thiamin from an... -

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Basic information

Entry
Database: PDB / ID: 3rlb
TitleCrystal structure at 2.0 A of the S-component for thiamin from an ECF-type ABC transporter
ComponentsThiT
KeywordsTHIAMINE-BINDING PROTEIN / S-component / ECF transporter / ABC transporter / Substrate-binding domain / membrane
Function / homologyArp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha / Chem-VIB / :
Function and homology information
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsErkens, G.B. / Berntsson, R.P.-A. / Fulyani, F. / Majsnerowska, M. / Vujicic-Zagar, A. / ter Beek, J. / Poolman, B. / Slotboom, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: The structural basis of modularity in ECF-type ABC transporters.
Authors: Erkens, G.B. / Berntsson, R.P. / Fulyani, F. / Majsnerowska, M. / Ter Beek, J. / Poolman, B. / Slotboom, D.J.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 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 / 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: ThiT
B: ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,36415
Polymers42,4632
Non-polymers3,90113
Water1,29772
1
A: ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6429
Polymers21,2311
Non-polymers2,4108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ThiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7226
Polymers21,2311
Non-polymers1,4915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.654, 84.654, 127.301
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 6 / Auth seq-ID: 7 - 182 / Label seq-ID: 17 - 192

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

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Components

#1: Protein ThiT


Mass: 21231.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Strain: NZ9000 / Gene: LLNZ_01755
Production host: Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Strain (production host): NZ9000 / References: UniProt: D8KFM5
#2: 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.: 11
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1 / Thiamine


Mass: 265.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N4OS / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 17% PEG3350, 0.2 M ammonium nitrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 / Wavelength: 0.9758, 0.9793, 0.9791
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.072251
20.97581
30.97931
40.97911
ReflectionNumber: 146525 / Rmerge(I) obs: 0.041 / D res high: 2.14 Å / Num. obs: 48470 / % possible obs: 65.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.3647.58527989910.03
4.526.36501598.810.034
3.694.52643598.510.036
3.23.69763098.810.047
2.863.2871799.610.065
2.622.86795382.110.087
2.422.62566454.110.136
2.272.4232822910.214
2.142.279768.110.439
ReflectionResolution: 2→47.585 Å / Num. all: 43288 / Num. obs: 43288 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Rsym value: 0.068 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.12 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.618 / % possible all: 96.6

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.71 / FOM acentric: 0.72 / FOM centric: 0.68 / Reflection: 15288 / Reflection acentric: 14532 / Reflection centric: 756
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.3-47.5850.930.940.8668860187
5.2-8.30.840.850.8220521901151
4.1-5.20.860.870.7725612435126
3.6-4.10.80.80.7425662452114
3.1-3.60.650.650.5445624379183
2.9-3.10.460.470.372859276495

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVEphasing
RESOLVE2.15phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→47.58 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.958 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23045 2165 5 %RANDOM
Rwork0.20577 ---
obs0.20701 41123 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.193 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20.02 Å2
2--0.04 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 194 72 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223021
X-RAY DIFFRACTIONr_bond_other_d0.0010.022075
X-RAY DIFFRACTIONr_angle_refined_deg1.6332.0174086
X-RAY DIFFRACTIONr_angle_other_deg1.13435086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4695353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45921.39586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03115452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.002158
X-RAY DIFFRACTIONr_chiral_restr0.1340.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023085
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02643
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7991.51751
X-RAY DIFFRACTIONr_mcbond_other0.2631.5724
X-RAY DIFFRACTIONr_mcangle_it1.35322821
X-RAY DIFFRACTIONr_scbond_it2.22531270
X-RAY DIFFRACTIONr_scangle_it3.3694.51265
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2264 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.495
loose thermal1.3510
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 150 -
Rwork0.28 2856 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 30.0355 Å / Origin y: -14.4828 Å / Origin z: 32.143 Å
111213212223313233
T0.0172 Å20.0039 Å2-0.0212 Å2-0.0736 Å20.0157 Å2--0.1134 Å2
L1.1666 °2-0.1374 °2-0.3581 °2-1.4109 °20.9127 °2--3.3596 °2
S-0.1034 Å °-0.0146 Å °0.0385 Å °-0.0095 Å °0.0941 Å °0.0502 Å °-0.0975 Å °-0.128 Å °0.0092 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 182
2X-RAY DIFFRACTION1B6 - 182
3X-RAY DIFFRACTION1A192 - 228
4X-RAY DIFFRACTION1B188 - 223
5X-RAY DIFFRACTION1A183 - 189
6X-RAY DIFFRACTION1B183 - 186
7X-RAY DIFFRACTION1A191
8X-RAY DIFFRACTION1B187

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