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- PDB-3brs: Crystal structure of sugar transporter from Clostridium phytoferm... -

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Basic information

Entry
Database: PDB / ID: 3brs
TitleCrystal structure of sugar transporter from Clostridium phytofermentans
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / sugar transporter / PSI-2
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Periplasmic binding protein/LacI transcriptional regulator / :
Function and homology information
Biological speciesClostridium phytofermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMalashkevich, V.N. / Patskovsky, Y. / Toro, R. / Meyers, A.J. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of sugar transporter from Clostridium phytofermentans.
Authors: Malashkevich, V.N. / Patskovsky, Y. / Toro, R. / Meyers, A.J. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic binding protein/LacI transcriptional regulator
B: Periplasmic binding protein/LacI transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)64,6602
Polymers64,6602
Non-polymers00
Water4,774265
1
A: Periplasmic binding protein/LacI transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)32,3301
Polymers32,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic binding protein/LacI transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)32,3301
Polymers32,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.620, 54.700, 90.240
Angle α, β, γ (deg.)90.00, 111.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic binding protein/LacI transcriptional regulator


Mass: 32330.143 Da / Num. of mol.: 2 / Fragment: Residues 32-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phytofermentans (bacteria) / Strain: ISDg / Gene: CphyDRAFT_2568 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q1FMG2, UniProt: A9KIC5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 294 K / pH: 5.5
Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350, cryoprotected in 20% Glycerol, VAPOR DIFFUSION, temperature 294K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionRedundancy: 2.4 % / Av σ(I) over netI: 3.9 / Number: 191431 / Rmerge(I) obs: 0.109 / Χ2: 0.88 / D res high: 2 Å / D res low: 50 Å / Num. obs: 80628 / % possible obs: 97.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315098.410.082.0772.6
3.424.3199.610.091.6362.6
2.993.429910.1121.1052.5
2.712.9997.510.1420.8572.3
2.522.7197.110.190.7232.3
2.372.529710.2310.5592.3
2.252.3797.210.2770.4512.3
2.152.259810.3170.3232.3
2.072.159810.3680.2872.3
22.0797.410.440.2372.2
ReflectionResolution: 2→50 Å / Num. obs: 80628 / % possible obs: 97.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 3.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.44 / % possible all: 97.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.388 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28284 2121 5.1 %RANDOM
Rwork0.20339 ---
obs0.20744 39783 99.22 %-
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 mean: 37.538 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 0 265 4473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224263
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.9935737
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2995540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02126.552174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16315841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0081510
X-RAY DIFFRACTIONr_chiral_restr0.1860.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023064
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.22135
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.22941
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3261.52798
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.485204329
X-RAY DIFFRACTIONr_scbond_it13.773201704
X-RAY DIFFRACTIONr_scangle_it6.9554.51407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 167 -
Rwork0.234 2682 -
obs--93.56 %
Refinement TLS params.Method: refined / Origin x: 51.2759 Å / Origin y: 37.003 Å / Origin z: 19.2784 Å
111213212223313233
T-0.0593 Å20.0217 Å20.0045 Å2-0.0014 Å20.0042 Å2---0.0818 Å2
L0.4102 °20.1465 °2-0.0094 °2-1.0487 °20.0181 °2--0.2986 °2
S-0.0245 Å °-0.0458 Å °0.0022 Å °-0.0096 Å °0.0315 Å °0.0168 Å °0.0018 Å °0.0019 Å °-0.007 Å °

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