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- PDB-4ys6: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (I... -

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Database: PDB / ID: 4ys6
TitleCRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM CLOSTRIDIUM PHYTOFERMENTANS (Cphy_1585, TARGET EFI-511156) WITH BOUND BETA-D-GLUCOSE
ComponentsPutative solute-binding component of ABC transporter
KeywordsSOLUTE-BINDING PROTEIN / ABC TRANSPORTER / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / beta-D-glucopyranose / Putative solute-binding component of ABC transporter
Function and homology information
Biological speciesClostridium phytofermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.698 Å
AuthorsVetting, M.W. / Patskovsky, Y. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. ...Vetting, M.W. / Patskovsky, Y. / 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 AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM CLOSTRIDIUM PHYTOFERMENTANS (Cphy_1585, TARGET EFI-511156) WITH BOUND BETA-D-GLUCOSE
Authors: Vetting, M.W. / Patskovsky, Y. / 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. / ...Authors: Vetting, M.W. / Patskovsky, Y. / 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 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: chem_comp / entity_src_gen ...chem_comp / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list / reflns / reflns_shell
Item: _chem_comp.type / _entity_src_gen.pdbx_alt_source_flag ..._chem_comp.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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.ptnr2_symmetry
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 solute-binding component of ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0129
Polymers39,6461
Non-polymers3668
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.686, 80.686, 170.004
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-697-

HOH

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Components

#1: Protein Putative solute-binding component of ABC transporter


Mass: 39646.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg) (bacteria)
Strain: ATCC 700394 / DSM 18823 / ISDg / Gene: Cphy_1585 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9KQP6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-BGC / beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 5 mM D-glucose); Reservoir (MCSG2 B1)(1.1 M Sodium Malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5 %(v/v) Jeffamine ED-2001 pH 7.0); Cryoprotection (100% Reservoir, dehydration)

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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: Feb 11, 2015 / 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: 1.698→100 Å / Num. obs: 36742 / % possible obs: 99.8 % / Redundancy: 11.7 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.01 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.03305 / Net I/σ(I): 20.3 / Num. measured all: 2098044 / Scaling rejects: 509
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible allCC1/2Rpim(I) all
1.69-1.731102.46547202399.4
7.12-32.8634.20.22925.52109761698.70.9670.041

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.698→23.938 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1825 1077 2.92 %
Rwork0.1495 35758 -
obs0.1504 36742 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.64 Å2 / Biso mean: 24.5065 Å2 / Biso min: 8.49 Å2
Refinement stepCycle: final / Resolution: 1.698→23.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 19 197 2679
Biso mean--20.69 35.16 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012538
X-RAY DIFFRACTIONf_angle_d1.2543442
X-RAY DIFFRACTIONf_chiral_restr0.049393
X-RAY DIFFRACTIONf_plane_restr0.006447
X-RAY DIFFRACTIONf_dihedral_angle_d13.029924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.698-1.77530.27151200.21374328444898
1.7753-1.86880.23371430.173243564499100
1.8688-1.98590.19031440.145443844528100
1.9859-2.13910.151210.126844384559100
2.1391-2.35420.1651340.122144404574100
2.3542-2.69450.16391280.135345034631100
2.6945-3.39320.16731420.153245264668100
3.3932-23.94090.19241450.157447834928100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5546-0.40080.12950.9575-0.181.1555-0.0198-0.10730.25910.0264-0.00710.0096-0.1398-0.04950.02720.1824-0.00150.0060.1655-0.02280.1844-29.502551.859314.494
21.6071-0.9483-0.36971.16870.15580.24050.02570.001-0.03240.0228-0.02030.1102-0.0381-0.1074-0.00020.11690.00340.01010.16510.00560.1226-33.751339.063611.2394
32.1516-0.8843-0.47151.76431.00632.83230.0170.0292-0.31070.10750.0080.01050.3058-0.05620.00210.1172-0.03140.00210.08770.02210.1692-15.452820.14329.2484
41.0221-0.18890.14141.1750.28380.8926-0.0023-0.1082-0.18630.15460.0528-0.03420.05210.0777-0.03960.0985-0.0077-0.00380.09870.02510.113-14.887625.020215.0791
50.90780.00670.31980.36630.00210.49870.01350.14310.0502-0.0473-0.0265-0.0324-0.08770.06360.00490.1466-0.00420.01320.16620.01390.1392-21.770239.90782.6582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 69 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 134 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 155 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 239 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 339 )A0

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