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- PDB-4c0r: Molecular and structural basis of glutathione import in Gram-posi... -

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Basic information

Entry
Database: PDB / ID: 4c0r
TitleMolecular and structural basis of glutathione import in Gram-positive bacteria via GshT and the cystine ABC importer TcyBC of Streptococcus mutans.
ComponentsPUTATIVE AMINO ACID BINDING PROTEIN
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / OXIDIZED GLUTATHIONE DISULFIDE / : / AtmA
Similarity search - Component
Biological speciesSTREPTOCOCCUS MUTANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.547 Å
AuthorsVergauwen, B. / Verstraete, K. / Senadheera, D.B. / Dansercoer, A. / Cvitkovitch, D.G. / Guedon, E. / Savvides, S.N.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Molecular and Structural Basis of Glutathione Import in Gram-Positive Bacteria Via Gsht and the Cystine Abc Importer Tcybc of Streptococcus Mutans.
Authors: Vergauwen, B. / Verstraete, K. / Senadheera, D.B. / Dansercoer, A. / Cvitkovitch, D.G. / Guedon, E. / Savvides, S.N.
History
DepositionAug 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Atomic model
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE AMINO ACID BINDING PROTEIN
B: PUTATIVE AMINO ACID BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,04950
Polymers57,1152
Non-polymers5,93448
Water12,088671
1
A: PUTATIVE AMINO ACID BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,82029
Polymers28,5571
Non-polymers3,26328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PUTATIVE AMINO ACID BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,82029
Polymers28,5571
Non-polymers3,26328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-252 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.040, 103.120, 64.090
Angle α, β, γ (deg.)90.00, 92.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PUTATIVE AMINO ACID BINDING PROTEIN / GSHT


Mass: 28557.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS MUTANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M2L4D8, UniProt: Q93DA5*PLUS
#2: Chemical ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE / Glutathione disulfide


Mass: 612.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#3: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.14 Å3/Da / Density % sol: 42.59 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1 M CADMIUM CHLORIDE HYDRATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 30% V/V POLYETHYLENE GLYCOL 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00, 1.55
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.551
ReflectionResolution: 1.55→37 Å / Num. obs: 69164 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.21
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 96.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.89 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q2C

2q2c


Resolution: 1.547→37.01 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 16.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1831 3458 5 %
Rwork0.1554 --
obs0.1568 69148 98.89 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.092 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.2583 Å20 Å20.9598 Å2
2--0.014 Å20 Å2
3---0.2444 Å2
Refinement stepCycle: LAST / Resolution: 1.547→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 112 671 4464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173875
X-RAY DIFFRACTIONf_angle_d1.6925271
X-RAY DIFFRACTIONf_dihedral_angle_d12.8591396
X-RAY DIFFRACTIONf_chiral_restr0.284595
X-RAY DIFFRACTIONf_plane_restr0.009687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5471-1.56830.2421240.21162361X-RAY DIFFRACTION90
1.5683-1.59070.25791360.20832588X-RAY DIFFRACTION98
1.5907-1.61440.21661410.20362666X-RAY DIFFRACTION99
1.6144-1.63970.23161350.19022583X-RAY DIFFRACTION99
1.6397-1.66650.23881370.18792603X-RAY DIFFRACTION99
1.6665-1.69530.22651390.18512632X-RAY DIFFRACTION99
1.6953-1.72610.21631380.1792618X-RAY DIFFRACTION99
1.7261-1.75930.19291390.16672642X-RAY DIFFRACTION99
1.7593-1.79520.20421360.162583X-RAY DIFFRACTION99
1.7952-1.83420.17651390.15452647X-RAY DIFFRACTION99
1.8342-1.87690.19191400.14742650X-RAY DIFFRACTION100
1.8769-1.92380.17791380.15592634X-RAY DIFFRACTION99
1.9238-1.97590.16981390.14832632X-RAY DIFFRACTION99
1.9759-2.0340.18251390.13982647X-RAY DIFFRACTION99
2.034-2.09960.15381380.14322623X-RAY DIFFRACTION99
2.0996-2.17470.16641410.1372675X-RAY DIFFRACTION99
2.1747-2.26170.19371360.142593X-RAY DIFFRACTION100
2.2617-2.36470.17211410.14012671X-RAY DIFFRACTION100
2.3647-2.48930.17811400.14142667X-RAY DIFFRACTION100
2.4893-2.64520.17651400.14482658X-RAY DIFFRACTION100
2.6452-2.84940.18171390.1472643X-RAY DIFFRACTION100
2.8494-3.1360.17211410.14822670X-RAY DIFFRACTION100
3.136-3.58950.15551390.152649X-RAY DIFFRACTION100
3.5895-4.52110.1691410.14232672X-RAY DIFFRACTION100
4.5211-37.02050.19481420.18342683X-RAY DIFFRACTION99

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