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- PDB-3i6v: Crystal structure of a periplasmic His/Glu/Gln/Arg/opine family-b... -

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Basic information

Entry
Database: PDB / ID: 3i6v
TitleCrystal structure of a periplasmic His/Glu/Gln/Arg/opine family-binding protein from Silicibacter pomeroyi in complex with lysine
Componentsperiplasmic His/Glu/Gln/Arg/opine family-binding protein
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / TRANSPORTER / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / membrane
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LYSINE / His/Glu/Gln/Arg/opine family ABC transporter, periplasmic His/Glu/Gln/Arg/opine family-binding protein
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Miller, S. / Romero, R. / 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 a periplasmic His/Glu/Gln/Arg/opine family-binding protein from Silicibacter pomeroyi in complex with lysine
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Miller, S. / Romero, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 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 His/Glu/Gln/Arg/opine family-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1884
Polymers24,9251
Non-polymers2623
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.931, 70.931, 141.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein periplasmic His/Glu/Gln/Arg/opine family-binding protein / His/Glu/Gln/Arg/opine family ABC transporter


Mass: 24925.369 Da / Num. of mol.: 1 / Fragment: sequence database residues 50-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: SPO1306 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LTV6
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.6
Details: 100mM sodium acetate pH 4.6, 25% PEG 6K, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2→31.699 Å / Num. all: 25236 / Num. obs: 25211 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.6 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 17.1 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 6.4 / Num. unique all: 3592 / Rsym value: 0.464 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.861 / SU B: 2.979 / SU ML: 0.084 / SU R Cruickshank DPI: 0.13 / SU Rfree: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1270 5.1 %RANDOM
Rwork0.198 ---
obs0.2 25131 99.9 %-
all-25156 --
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 max: 55.97 Å2 / Biso mean: 28.385 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 17 77 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221694
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9622306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5665225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88325.51378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06615264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.423158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211314
X-RAY DIFFRACTIONr_mcbond_it0.8781.51089
X-RAY DIFFRACTIONr_mcangle_it1.61421745
X-RAY DIFFRACTIONr_scbond_it2.573605
X-RAY DIFFRACTIONr_scangle_it4.0284.5557
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 100 -
Rwork0.247 1688 -
all-1788 -
obs-1688 99.67 %

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