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- PDB-4oen: Crystal structure of the second substrate binding domain of a put... -

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Basic information

Entry
Database: PDB / ID: 4oen
TitleCrystal structure of the second substrate binding domain of a putative amino acid ABC transporter from Streptococcus pneumoniae Canada MDR_19A
ComponentsSecond substrate binding domain of putative amino acid ABC transporter
KeywordsTRANSPORT PROTEIN / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / ALPHA AND BETA PROTEIN / PERIPLASMIC BINDING PROTEIN TYPE II FOLD / SUBSTRATE BINDING DOMAIN OF PUTATIVE AMINO ACID ABC TRANSPORTER SYSTEM
Function / homology
Function and homology information


amino acid transport / ligand-gated monoatomic ion channel activity / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
ABC transporter membrane protein permease protein ArtM/GltK/GlnP/TcyL/YhdX-like / Amino acid ABC transporter, permease protein, 3-TM domain / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / 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 ...ABC transporter membrane protein permease protein ArtM/GltK/GlnP/TcyL/YhdX-like / Amino acid ABC transporter, permease protein, 3-TM domain / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / 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
ACETATE ION / Amino acid ABC transporter, amino acid-binding protein/permease protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of the second substrate binding domain of a putative amino acid ABC transporter from Streptococcus pneumoniae Canada MDR_19A
Authors: Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Second substrate binding domain of putative amino acid ABC transporter
B: Second substrate binding domain of putative amino acid ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,62318
Polymers47,7932
Non-polymers83016
Water14,196788
1
A: Second substrate binding domain of putative amino acid ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2768
Polymers23,8971
Non-polymers3807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Second substrate binding domain of putative amino acid ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,34710
Polymers23,8971
Non-polymers4509
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.432, 109.606, 57.922
Angle α, β, γ (deg.)90.00, 111.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Second substrate binding domain of putative amino acid ABC transporter


Mass: 23896.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: SpneCM_010100001889 / Plasmid: P15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2UQ91*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 788 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.5 M ammonium sulfate, 0.1 M sodium acetate pH4.6, 2% Hexandiol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 58402 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.9 % / Rsym value: 0.116 / Net I/σ(I): 10.85
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.13 / Rsym value: 0.65 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: dev_1538)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WDN

1wdn


Resolution: 1.65→27.401 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 2954 5.06 %random
Rwork0.1608 ---
obs0.1626 58367 98.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→27.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 42 788 4170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073489
X-RAY DIFFRACTIONf_angle_d1.054723
X-RAY DIFFRACTIONf_dihedral_angle_d11.8431287
X-RAY DIFFRACTIONf_chiral_restr0.043528
X-RAY DIFFRACTIONf_plane_restr0.005620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6498-1.67680.25081390.22242463X-RAY DIFFRACTION93
1.6768-1.70580.24331280.22412686X-RAY DIFFRACTION99
1.7058-1.73680.24191240.20962609X-RAY DIFFRACTION99
1.7368-1.77020.21341630.20192646X-RAY DIFFRACTION98
1.7702-1.80630.25481340.19092607X-RAY DIFFRACTION99
1.8063-1.84560.21891400.17952612X-RAY DIFFRACTION98
1.8456-1.88850.21311480.16742601X-RAY DIFFRACTION97
1.8885-1.93570.23571420.18342608X-RAY DIFFRACTION97
1.9357-1.9880.18331280.1642591X-RAY DIFFRACTION98
1.988-2.04650.20871370.16572602X-RAY DIFFRACTION97
2.0465-2.11250.20221470.162606X-RAY DIFFRACTION98
2.1125-2.1880.20791400.16252630X-RAY DIFFRACTION98
2.188-2.27560.20271350.17852637X-RAY DIFFRACTION99
2.2756-2.37910.18191210.15632733X-RAY DIFFRACTION100
2.3791-2.50440.19691580.16272654X-RAY DIFFRACTION100
2.5044-2.66120.23461360.16952699X-RAY DIFFRACTION100
2.6612-2.86650.20721430.16882666X-RAY DIFFRACTION100
2.8665-3.15460.19331490.16082659X-RAY DIFFRACTION100
3.1546-3.61020.1861350.13912722X-RAY DIFFRACTION100
3.6102-4.54510.15171570.13012668X-RAY DIFFRACTION100
4.5451-27.40530.18871500.15862714X-RAY DIFFRACTION99
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)
13.0383-0.05330.34413.7172-0.30964.0554-0.0371-0.10240.10040.1216-0.0343-0.144-0.02950.26740.04710.0683-0.0307-0.02310.1595-0.01710.129311.7178-1.608423.6915
20.78950.63340.00663.2651-0.02980.3875-0.0034-0.00980.0007-0.0499-0.07280.04080.0786-0.04590.07650.1012-0.00910.0130.1433-0.02150.102-1.0633-21.755819.0688
31.5378-0.9158-0.67492.48861.13184.52040.07460.15210.1032-0.40810.0073-0.0118-0.27520.0105-0.07540.1313-0.0441-0.02150.1720.01520.17327.0366-0.675911.2655
43.1934-0.31190.54042.2725-0.51314.4261-0.1551-0.199-0.21510.17420.10870.15030.142-0.07310.03460.10980.01330.04750.11860.02550.1252-10.427228.755415.6577
50.64810.1910.01153.62030.29110.4918-0.0476-0.0370.0014-0.26770.0242-0.0827-0.05410.12010.02580.1225-0.00060.00730.140.02360.10660.16349.857311.5718
64.1404-2.03861.57872.9905-1.58546.17920.04520.2656-0.2602-0.4188-0.0991-0.13660.28420.15410.03280.0936-0.0380.05580.1239-0.01310.148-5.824128.48063.178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 266:333
2X-RAY DIFFRACTION2chain A and resi 334:456
3X-RAY DIFFRACTION3chain A and resi 457:487
4X-RAY DIFFRACTION4chain B and resi 266:333
5X-RAY DIFFRACTION5chain B and resi 334:456
6X-RAY DIFFRACTION6chain B and resi 457:487

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