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- PDB-4i62: 1.05 Angstrom crystal structure of an amino acid ABC transporter ... -

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Basic information

Entry
Database: PDB / ID: 4i62
Title1.05 Angstrom crystal structure of an amino acid ABC transporter substrate-binding protein AbpA from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein, putative
KeywordsTRANSPORT PROTEIN / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES (NIAID) / NIAID / National Institute of Allergy and Infectious Diseases / alpha and beta protein / periplasmic binding protein type ii fold / putative amino acid abc transporter system substrate binding protein / l-arginine / putative membrane-anchored lipoprotein
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / membrane
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / Amino acid ABC transporter, periplasmic amino acid-binding protein, putative / Amino acid ABC transporter, periplasmic amino acid-binding protein, putative
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsStogios, P.J. / Kudritska, M. / Wawrzak, Z. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.05 Angstrom crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine
Authors: Stogios, P.J. / Kudritska, M. / Wawrzak, Z. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Structure summary
Revision 1.2Sep 20, 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: Amino acid ABC transporter, periplasmic amino acid-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5474
Polymers29,3011
Non-polymers2463
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.682, 55.028, 46.673
Angle α, β, γ (deg.)90.00, 114.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amino acid ABC transporter, periplasmic amino acid-binding protein, putative


Mass: 29300.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: SpneCM_010100008960 / Plasmid: p15Tv-Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04MW8, UniProt: A0A0H2ZN67*PLUS
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1.93 Å3/Da / Density % sol: 27.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 30% Jeffamine ED-2001 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. obs: 91003 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.5 % / Rsym value: 0.044 / Net I/σ(I): 30.58
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.58 / Num. unique all: 4332 / Rsym value: 0.607 / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDN

1wdn


Resolution: 1.05→23.072 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 1999 2.2 %random
Rwork0.1659 ---
obs0.1662 90970 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→23.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 14 337 2163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112051
X-RAY DIFFRACTIONf_angle_d1.4572790
X-RAY DIFFRACTIONf_dihedral_angle_d13.655831
X-RAY DIFFRACTIONf_chiral_restr0.093325
X-RAY DIFFRACTIONf_plane_restr0.008365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0502-1.07650.29491330.26575983X-RAY DIFFRACTION93
1.0765-1.10560.25631450.23316368X-RAY DIFFRACTION99
1.1056-1.13810.22291420.20596352X-RAY DIFFRACTION100
1.1381-1.17490.18671460.19256365X-RAY DIFFRACTION100
1.1749-1.21690.19611370.18236411X-RAY DIFFRACTION100
1.2169-1.26560.19271490.17596405X-RAY DIFFRACTION100
1.2656-1.32320.20731410.17086343X-RAY DIFFRACTION100
1.3232-1.39290.17051510.17136435X-RAY DIFFRACTION100
1.3929-1.48020.19261360.16466389X-RAY DIFFRACTION100
1.4802-1.59440.18471490.15596397X-RAY DIFFRACTION100
1.5944-1.75490.17381380.15566418X-RAY DIFFRACTION100
1.7549-2.00870.18981460.1576425X-RAY DIFFRACTION100
2.0087-2.53020.16241460.15436459X-RAY DIFFRACTION100
2.5302-23.07790.16171400.16066221X-RAY DIFFRACTION95
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)
11.86390.2498-0.43321.1674-0.14861.61890.0518-0.1764-0.05650.045-0.0618-0.0570.06010.02670.01310.0583-0.0079-0.01270.0574-0.00140.055814.296423.796539.7171
21.30960.6771-0.7341.4011-0.97351.6004-0.01880.0941-0.0209-0.0826-0.0148-0.02680.01740.01970.03140.06680.0067-0.01650.0626-0.00220.065125.941931.760421.7286
32.32041.1523-0.08574.4757-1.09671.80290.0210.02950.2208-0.19910.05610.4155-0.0299-0.173-0.05460.05920.0196-0.00390.1042-0.02910.06044.187926.693533.5903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 31:125
2X-RAY DIFFRACTION2chain A and resi 126:232
3X-RAY DIFFRACTION3chain A and resi 233:268

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