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- PDB-4wzz: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (I... -

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Entry
Database: PDB / ID: 4wzz
TitleCRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM CLOSTRIDIUM PHYTOFERMENTAS (Cphy_0583, TARGET EFI-511148) WITH BOUND L-RHAMNOSE
ComponentsPutative sugar ABC transporter, substrate-binding protein
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Autoinducer 2 ABC transporter, substrate-binding protein LsrB / 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
alpha-L-rhamnopyranose / Autoinducer 2-binding protein LsrB
Similarity search - Component
Biological speciesClostridium phytofermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, 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 AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM CLOSTRIDIUM PHYTOFERMENTAS (Cphy_0583, TARGET EFI-511148) WITH BOUND L-RHAMNOSE
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, 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
DepositionNov 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Mar 15, 2017Group: Other
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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: Putative sugar ABC transporter, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6484
Polymers39,3591
Non-polymers2883
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.625, 87.625, 83.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

21A-568-

HOH

Detailsbiological unit is a monomer

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Components

#1: Protein Putative sugar ABC transporter, substrate-binding protein


Mass: 39359.352 Da / Num. of mol.: 1 / Fragment: ABC TRANSPORTER SOLUTE BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phytofermentans (bacteria) / Strain: ATCC 700394 / DSM 18823 / ISDg / Gene: Cphy_0583 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9KIX1
#2: Sugar ChemComp-RAM / alpha-L-rhamnopyranose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 39.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (51.24 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM L-RHAMNOSE); Reservoir (0.1 M Sodium Hepes pH 7.5, 1.4 M Sodium Citrate); Cryoprotection (80% Reservoir + 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→87.62 Å / Num. obs: 36564 / % possible obs: 100 % / Redundancy: 28.6 % / Biso Wilson estimate: 16.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.037 / Net I/σ(I): 13.9 / Num. measured all: 1855141 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
1.4-1.4227.90.455418757831420.2770.874
7.67-87.6222.90.08746.3112684920.9920.018

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.1.27data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→26.666 Å / FOM work R set: 0.9145 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 1827 5 %
Rwork0.1454 34737 -
obs0.1471 36564 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.56 Å2 / Biso mean: 22.01 Å2 / Biso min: 6.38 Å2
Refinement stepCycle: final / Resolution: 1.7→26.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 43 305 2714
Biso mean--21.75 31.92 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092446
X-RAY DIFFRACTIONf_angle_d1.2253333
X-RAY DIFFRACTIONf_chiral_restr0.072390
X-RAY DIFFRACTIONf_plane_restr0.006437
X-RAY DIFFRACTIONf_dihedral_angle_d13.562872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.7460.19661320.160826322764
1.746-1.79730.21621560.157926142770
1.7973-1.85530.21081330.163226272760
1.8553-1.92160.19651320.150626412773
1.9216-1.99860.17861320.148926582790
1.9986-2.08950.16651270.136726342761
2.0895-2.19960.18271330.136726572790
2.1996-2.33730.15441450.137126482793
2.3373-2.51770.2031470.147126532800
2.5177-2.77080.18121520.149626702822
2.7708-3.17120.18841590.152426742833
3.1712-3.99320.17461520.132727302882
3.9932-26.66950.16551270.148928993026
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9082-0.1577-0.01841.3847-0.80481.52030.1478-0.2588-0.24580.3202-0.1220.0603-0.0093-0.1068-0.03430.2239-0.0994-0.03390.17180.03630.17359.550634.468232.4707
21.03730.14880.27481.01110.1650.92030.1914-0.22780.0860.4206-0.1969-0.0341-0.1797-0.0630.04780.2087-0.0764-0.03890.137-0.01510.123167.862849.882227.34
31.70810.12380.35131.2417-0.22591.7170.02660.09540.1587-0.0005-0.02690.0772-0.1872-0.13820.02680.08620.0227-0.00450.0683-0.00340.107961.833455.989113.1853
41.20240.24430.28451.3087-0.3881.42260.08870.0544-0.0891-0.1403-0.0614-0.08780.1425-0.0469-0.02120.0955-0.0047-0.00960.0726-0.00870.11167.249544.321512.1466
50.3816-0.2133-0.01510.2869-0.02030.11490.1408-0.0897-0.24010.0308-0.1391-0.23310.07450.1743-0.13150.4301-0.182-0.39310.55780.2290.457779.955833.707637.2115
60.78690.50030.26031.309-0.2710.77450.2613-0.129-0.2630.2196-0.5533-0.6390.08050.4385-0.3120.1259-0.1048-0.15540.16340.01130.13876.235840.035622.5242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 121 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 201 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 233 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 310 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 333 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 334 through 367 )A0

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