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- PDB-4nmy: Crystal Structure of the Thiamin-bound form of Substrate-binding ... -

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Basic information

Entry
Database: PDB / ID: 4nmy
TitleCrystal Structure of the Thiamin-bound form of Substrate-binding Protein of ABC Transporter from Clostridium difficile
ComponentsABC-type transport system, extracellular solute-binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / SBP fold
Function / homology
Function and homology information


thiamine biosynthetic process
Similarity search - Function
NMT1/THI5 family / SsuA/THI5-like / NMT1/THI5 like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-VIB / ABC-type transport system, extracellular solute-binding protein
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.896 Å
AuthorsKim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.
Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / ...Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / Minor, W. / Joachimiak, A. / Savchenko, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 25, 2026Group: 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.page_first / _citation.page_last / _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: ABC-type transport system, extracellular solute-binding protein
B: ABC-type transport system, extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2564
Polymers68,7262
Non-polymers5312
Water7,548419
1
A: ABC-type transport system, extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6282
Polymers34,3631
Non-polymers2651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC-type transport system, extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6282
Polymers34,3631
Non-polymers2651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.529, 76.867, 154.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC-type transport system, extracellular solute-binding protein


Mass: 34362.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_19790 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q187U0
#2: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1


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


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.2 M ammonium sulfate, 0.1 M sodium succinate pH7.5, 0.96 % LDAO, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 47478 / Num. obs: 47478 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 19.33 Å2 / Rsym value: 0.085 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2273 / Rsym value: 0.581 / % possible all: 98.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.896→38.433 Å / SU ML: 0.19 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2368 5.05 %random
Rwork0.164 ---
obs0.166 46934 98.25 %-
all-46934 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.25 Å2
Refinement stepCycle: LAST / Resolution: 1.896→38.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 36 419 5221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084918
X-RAY DIFFRACTIONf_angle_d1.0976662
X-RAY DIFFRACTIONf_dihedral_angle_d14.3761816
X-RAY DIFFRACTIONf_chiral_restr0.077718
X-RAY DIFFRACTIONf_plane_restr0.004848
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8965-1.93520.26711180.2182089220780
1.9352-1.97720.27951550.212493264896
1.9772-2.02320.26311350.19722596273199
2.0232-2.07380.30291300.192619274999
2.0738-2.12990.2461440.187826102754100
2.1299-2.19260.22611320.17912640277299
2.1926-2.26330.24271560.17392607271399
2.2633-2.34420.19661260.173126592785100
2.3442-2.43810.21641400.172226152755100
2.4381-2.5490.21021240.167926692793100
2.549-2.68330.24841340.17126622796100
2.6833-2.85140.22971320.174426792811100
2.8514-3.07150.18011290.172426982827100
3.0715-3.38040.19911570.173326622819100
3.3804-3.86920.19321350.152727192854100
3.8692-4.87320.15151610.124527142875100
4.8732-38.44140.15321600.14152835299599

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