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- PDB-4eq9: 1.4 Angstrom Crystal Structure of ABC Transporter Glutathione-Bin... -

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Basic information

Entry
Database: PDB / ID: 4eq9
Title1.4 Angstrom Crystal Structure of ABC Transporter Glutathione-Binding Protein GshT from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Glutathione
ComponentsABC transporter substrate-binding protein-amino acid transport
KeywordsTRANSPORT PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / ABC transporter substrate-binding protein-amino acid transport
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMinasov, G. / Wawrzak, Z. / Stogios, P.J. / Light, S.H. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.4 Angstrom Crystal Structure of Putative ABC Transporter Substrate-Binding Protein from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Glutathione.
Authors: Minasov, G. / Wawrzak, Z. / Stogios, P.J. / Light, S.H. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein-amino acid transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0352
Polymers27,7281
Non-polymers3071
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.801, 42.391, 74.248
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ABC transporter substrate-binding protein-amino acid transport


Mass: 27728.049 Da / Num. of mol.: 1 / Fragment: UNP residues 34-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: ABC-SBP, spr0146 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8DRG2
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 0.3M Sodium chloride, 0.01M HEPES pH 7.5; Screen: 0.05M ADA (N-(2-Acetamido)iminodiacetic Acid) pH 7.0, 25% (w/v) PEG 3350; Cryo: paratone, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 51214 / Num. obs: 51214 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 28.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2565 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q2A

2q2a


Resolution: 1.4→27.03 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.17 / SU ML: 0.039
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18993 2587 5.1 %RANDOM
Rwork0.1677 ---
all0.16883 48586 --
obs0.16883 48586 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.692 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20.1 Å2
2--0 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 20 308 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222175
X-RAY DIFFRACTIONr_bond_other_d0.0010.021476
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9842969
X-RAY DIFFRACTIONr_angle_other_deg0.86233644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.865280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53525.926108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30815401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.688159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212526
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02418
X-RAY DIFFRACTIONr_mcbond_it1.1271.51321
X-RAY DIFFRACTIONr_mcbond_other0.3881.5525
X-RAY DIFFRACTIONr_mcangle_it1.75322169
X-RAY DIFFRACTIONr_scbond_it2.9133854
X-RAY DIFFRACTIONr_scangle_it4.5474.5800
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 182 -
Rwork0.231 3497 -
obs-3497 98.42 %
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)
11.64660.4353-0.05780.9238-0.03821.9647-0.03810.3511-0.1238-0.1575-0.0186-0.06590.13520.2990.05670.08630.0150.00360.1711-0.01040.027945.058324.649953.4235
22.24750.5801-0.77761.261-0.40372.02650.02420.34560.2613-0.0997-0.010.1286-0.2390.0785-0.01420.097-0.0147-0.02970.11870.04850.042537.320235.611753.4848
31.988-0.6599-0.9681.34050.14761.5125-0.0693-0.0111-0.02750.13380.01920.38640.0069-0.11960.050.04110.00270.04280.0152-0.0050.167320.597731.907973.7335
41.5533-0.4644-0.17471.63650.59180.9958-0.00030.00330.1726-0.052-0.04410.1316-0.0917-0.03360.04440.0535-0.00320.00580.004-0.01730.12329.832741.160371.4829
51.7115-1.0387-0.19853.35890.25751.0122-0.03660.0468-0.10580.07040.02680.42250.0544-0.07950.00980.0231-0.01170.02120.01180.00170.111626.358324.943669.1558
60.98840.455-0.12160.8799-0.44961.9299-0.10090.47470.0724-0.23430.03820.0686-0.011-0.00960.06270.15-0.0113-0.03750.28550.02120.019437.464830.087742.9194
72.03760.17860.11465.8967-1.96394.4068-0.07950.5212-0.0718-0.40130.1370.33860.2923-0.3404-0.05750.1332-0.055-0.0560.2507-0.04530.051528.463421.432647.4955
89.0086-1.6673-3.20899.0005-0.67831.3296-0.0203-0.1135-0.1650.0086-0.02580.15520.0040.04980.04620.0453-0.0156-0.01420.045-0.00510.06535.188530.55463.1813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 96
2X-RAY DIFFRACTION2A97 - 125
3X-RAY DIFFRACTION3A126 - 151
4X-RAY DIFFRACTION4A152 - 179
5X-RAY DIFFRACTION5A180 - 224
6X-RAY DIFFRACTION6A225 - 256
7X-RAY DIFFRACTION7A257 - 276
8X-RAY DIFFRACTION8A301

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