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- PDB-4z0n: Crystal Structure of a Periplasmic Solute binding protein (IPR025... -

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Entry
Database: PDB / ID: 4z0n
TitleCrystal Structure of a Periplasmic Solute binding protein (IPR025997) from Streptobacillus moniliformis DSM-12112 (Smon_0317, TARGET EFI-511281) with bound D-Galactose
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsTRANSCRIPTION / Periplasmic solute binding Protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / beta-D-galactopyranose / Periplasmic binding protein/LacI transcriptional regulator
Similarity search - Component
Biological speciesStreptobacillus moniliformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.26 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal Structure of a Periplasmic Solute binding protein (IPR025997) from Streptobacillus moniliformis DSM-12112 (Smon_0317, TARGET EFI-511281) with bound D-Galactose
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_symm_contact / struct_conn / struct_conn_type / struct_keywords / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_keywords.text
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,26610
Polymers37,5171
Non-polymers7499
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.396, 44.011, 62.037
Angle α, β, γ (deg.)90.000, 104.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Periplasmic binding protein/LacI transcriptional regulator


Mass: 37516.984 Da / Num. of mol.: 1
Fragment: Periplasmic Solute Binding Protein, UNP residues 19-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptobacillus moniliformis (bacteria)
Strain: ATCC 14647 / DSM 12112 / NCTC 10651 / 9901 / Gene: Smon_0317 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D1AWX5
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 454 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.05 Å3/Da / Density % sol: 40.06 % / Description: Brick rods
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (20 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Galactose); Reservoir (0.1 M Sodium acetate:HCl pH 4.5, 2.0 M Ammonium sulfate); Cryoprotection (80% 2M Lithium sulfate, 20% Reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 18, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 73384 / % possible obs: 88.57 % / Redundancy: 1 % / Biso Wilson estimate: 14.37 Å2 / Rmerge(I) obs: 0.092 / Net I/av σ(I): 15.561 / Net I/σ(I): 8 / Num. measured all: 301
Reflection shellRejects: 0

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.26→24.115 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.165 3593 4.9 %
Rwork0.1386 69791 -
obs0.1399 69792 88.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.64 Å2 / Biso mean: 19.8511 Å2 / Biso min: 10.49 Å2
Refinement stepCycle: final / Resolution: 1.26→24.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 63 451 2889
Biso mean--31.72 30.89 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052471
X-RAY DIFFRACTIONf_angle_d1.0393356
X-RAY DIFFRACTIONf_chiral_restr0.071379
X-RAY DIFFRACTIONf_plane_restr0.005437
X-RAY DIFFRACTIONf_dihedral_angle_d13.078923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.26-1.27380.247340.31961521565
1.2738-1.29130.2803370.241276680325
1.2913-1.30970.2724940.20571595168954
1.3097-1.32930.26951080.19192167227572
1.3293-1.350.22331160.17852441255780
1.35-1.37220.19051170.17782593271086
1.3722-1.39580.21131380.16422639277788
1.3958-1.42120.23061290.15962833296293
1.4212-1.44850.20661410.15332991313299
1.4485-1.47810.18681660.141529963162100
1.4781-1.51020.1851540.133230213175100
1.5102-1.54540.1681400.127830303170100
1.5454-1.5840.16911470.129630143161100
1.584-1.62680.17121560.123930493205100
1.6268-1.67470.15971630.123630273190100
1.6747-1.72870.14531610.122630103171100
1.7287-1.79050.14771740.128629893163100
1.7905-1.86210.17491430.129230253168100
1.8621-1.94690.14571780.128330413219100
1.9469-2.04940.14511630.12929943157100
2.0494-2.17780.14411580.131630533211100
2.1778-2.34580.15891540.134930403194100
2.3458-2.58160.17161560.150930723228100
2.5816-2.95460.17751770.157730343211100
2.9546-3.72030.15261460.138230763222100
3.7203-24.11980.16161730.130931433316100

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