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- PDB-4h5g: Crystal structure of an amino acid ABC transporter substrate-bind... -

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Basic information

Entry
Database: PDB / ID: 4h5g
TitleCrystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 2
ComponentsAmino acid ABC superfamily ATP binding cassette transporter, binding protein
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 / putative amino acid ABC transporter system substrate binding protein / amino acids / 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
ACETATE ION / ARGININE / DI(HYDROXYETHYL)ETHER / ABC transporter, substrate-binding protein, family 3
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 2
Authors: Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Other
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

Downloads & links

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Assembly

Deposited unit
A: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
B: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,76317
Polymers52,3512
Non-polymers1,41115
Water7,548419
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A: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,05511
Polymers26,1761
Non-polymers88010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7076
Polymers26,1761
Non-polymers5325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.600, 183.940, 62.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21B-401-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Amino acid ABC superfamily ATP binding cassette transporter, binding protein


Mass: 26175.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: HMPREF0837_11153, SpneCM_010100001092 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D6ZRZ2

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Non-polymers , 7 types, 434 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE ELECTRON DENSITY CLEARLY SUPPORTS HISTIDINE AT POSITION 136 RATHER THAN ARGININE. HOWEVER, NO ...THE ELECTRON DENSITY CLEARLY SUPPORTS HISTIDINE AT POSITION 136 RATHER THAN ARGININE. HOWEVER, NO SUITABLE SEQUENCE IN THE GENOME DATABASES WAS FOUND. HIS 136 IS ASSUMED TO BE A SEQUENCE MUTATION IN THE GENE WE WORKED WITH, RELATIVE TO THE DATABASE SEQUENCE D6ZRZ2.

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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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, PEG 2K MME 30% (w/v), 2% tacsimate, 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: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.78→91.97 Å / Num. obs: 54996 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.6
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.6 / Num. unique all: 61601 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDN

1wdn


Resolution: 1.78→91.97 Å / SU ML: 0.11 / Cross valid method: random / σ(F): 1.35 / Phase error: 16.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 2672 5.06 %throughout
Rwork0.1556 ---
obs0.1572 54973 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→91.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 91 419 4134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073874
X-RAY DIFFRACTIONf_angle_d1.1675231
X-RAY DIFFRACTIONf_dihedral_angle_d14.4711465
X-RAY DIFFRACTIONf_chiral_restr0.076614
X-RAY DIFFRACTIONf_plane_restr0.004687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80020.247820.22923301X-RAY DIFFRACTION100
1.8002-1.82140.2882830.22433406X-RAY DIFFRACTION100
1.8214-1.84360.2376900.20773343X-RAY DIFFRACTION100
1.8436-1.8670.2217890.20223382X-RAY DIFFRACTION100
1.867-1.89150.2246880.19623279X-RAY DIFFRACTION100
1.8915-1.91740.2154930.18443313X-RAY DIFFRACTION100
1.9174-1.94480.2064970.18913328X-RAY DIFFRACTION100
1.9448-1.97390.2243890.193323X-RAY DIFFRACTION100
1.9739-2.00470.24981000.17643337X-RAY DIFFRACTION100
2.0047-2.03760.2105920.16713309X-RAY DIFFRACTION100
2.0376-2.07270.2225960.16893359X-RAY DIFFRACTION100
2.0727-2.11040.1703810.14923350X-RAY DIFFRACTION100
2.1104-2.1510.1684860.15393326X-RAY DIFFRACTION100
2.151-2.19490.1925870.15383334X-RAY DIFFRACTION100
2.1949-2.24270.21061030.14793372X-RAY DIFFRACTION100
2.2427-2.29480.1866950.15693349X-RAY DIFFRACTION100
2.2948-2.35220.2049780.15293300X-RAY DIFFRACTION100
2.3522-2.41580.1938720.15913380X-RAY DIFFRACTION100
2.4158-2.48690.1879780.15123394X-RAY DIFFRACTION100
2.4869-2.56720.17361010.1423292X-RAY DIFFRACTION100
2.5672-2.6590.1816870.153363X-RAY DIFFRACTION100
2.659-2.76540.1652790.15093339X-RAY DIFFRACTION100
2.7654-2.89130.1696970.15613320X-RAY DIFFRACTION100
2.8913-3.04370.22031020.15233315X-RAY DIFFRACTION100
3.0437-3.23440.1976950.15423331X-RAY DIFFRACTION100
3.2344-3.48420.1785790.13993366X-RAY DIFFRACTION100
3.4842-3.83480.1507860.13413348X-RAY DIFFRACTION100
3.8348-4.38970.1399980.12233330X-RAY DIFFRACTION100
4.3897-5.53050.1562890.13983340X-RAY DIFFRACTION100
5.5305-92.0930.1894860.18283345X-RAY DIFFRACTION100
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)
13.92312.2551.52352.12121.22272.91190.1743-0.2721-0.24250.2007-0.1276-0.21090.25650.0521-0.00030.15750.021-0.00170.19510.03230.142449.32248.403935.9116
21.76790.95470.40371.7260.42630.6844-0.0363-0.01620.0061-0.12150.00280.18080.013-0.13090.04480.1521-0.01030.00350.1960.00770.130530.687747.060326.5312
31.35510.2123-0.12393.74531.61982.3451-0.02180.0374-0.0269-0.002-0.0147-0.04610.07550.00820.02670.12190.00490.00980.1810.02380.107548.332552.264525.5631
42.114-0.4009-0.98033.58610.26773.3479-0.06230.07550.1021-0.17510.11050.32490.0191-0.0513-0.04620.1621-0.011-0.03290.1175-0.00050.20326.214672.8782-5.3011
51.705-0.45240.09044.3076-0.16222.3731-0.1972-0.48910.02391.44620.27660.3349-0.1149-0.2197-0.0550.59370.10310.12370.2885-0.00320.248226.21775.839615.4837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 30:80 )A30 - 80
2X-RAY DIFFRACTION2( CHAIN A AND RESID 81:225 )A81 - 225
3X-RAY DIFFRACTION3( CHAIN A AND RESID 226:269 )A226 - 269
4X-RAY DIFFRACTION4( CHAIN B AND RESID 30:80 )B30 - 80
5X-RAY DIFFRACTION5( CHAIN B AND RESID 81:225 )B81 - 225

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