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- PDB-4h5f: Crystal structure of an amino acid ABC transporter substrate-bind... -

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Basic information

Entry
Database: PDB / ID: 4h5f
TitleCrystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 1
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 / TRIETHYLENE GLYCOL / ABC transporter, substrate-binding protein, family 3
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1
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 1.1Sep 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_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
C: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
D: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,56451
Polymers104,7024
Non-polymers4,86247
Water8,971498
1
A: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,95018
Polymers26,1761
Non-polymers1,77417
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)27,47014
Polymers26,1761
Non-polymers1,29413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,43013
Polymers26,1761
Non-polymers1,25412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Amino acid ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7146
Polymers26,1761
Non-polymers5395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.373, 61.705, 103.626
Angle α, β, γ (deg.)90.00, 118.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 26175.562 Da / Num. of mol.: 4
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 , 9 types, 545 molecules

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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#8: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, PEG 2K MME 30% (w/v), 2% PEG400, 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: Jun 30, 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: 1.9→91.461 Å / Num. all: 254378 / Num. obs: 85607 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.3 / Num. unique all: 36813 / % possible all: 99.2

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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: 1.9→91.461 Å / Cross valid method: random / σ(F): 1.35 / Phase error: 25.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 4300 5.3 %throughout
Rwork0.1644 ---
obs0.1658 85590 94.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→91.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7239 0 315 498 8052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087652
X-RAY DIFFRACTIONf_angle_d1.18510252
X-RAY DIFFRACTIONf_dihedral_angle_d14.4582904
X-RAY DIFFRACTIONf_chiral_restr0.071198
X-RAY DIFFRACTIONf_plane_restr0.0051347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93310.28522140.26467881X-RAY DIFFRACTION92
1.9331-1.96820.28352080.25127844X-RAY DIFFRACTION92
1.9682-2.00610.25742020.23877868X-RAY DIFFRACTION92
2.0061-2.0470.26152160.23137804X-RAY DIFFRACTION91
2.047-2.09150.24382200.22887739X-RAY DIFFRACTION91
2.0915-2.14010.26571960.21367799X-RAY DIFFRACTION91
2.1401-2.19360.22862070.21297781X-RAY DIFFRACTION91
2.1936-2.25290.22712180.20077762X-RAY DIFFRACTION90
2.2529-2.31910.23681680.20497789X-RAY DIFFRACTION91
2.3191-2.39390.22621940.19577752X-RAY DIFFRACTION91
2.3939-2.47940.21952210.18297745X-RAY DIFFRACTION90
2.4794-2.57850.23491710.18437694X-RAY DIFFRACTION91
2.5785-2.69570.21712080.17997674X-RAY DIFFRACTION90
2.6957-2.83770.20122060.16637636X-RAY DIFFRACTION89
2.8377-3.01520.18512100.15547603X-RAY DIFFRACTION89
3.0152-3.24750.1851930.14657644X-RAY DIFFRACTION89
3.2475-3.57340.16411960.13297562X-RAY DIFFRACTION89
3.5734-4.08840.15741840.12037565X-RAY DIFFRACTION89
4.0884-5.1430.15062250.10527484X-RAY DIFFRACTION87
5.143-24.42750.20112010.15257463X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 49.9538 Å / Origin y: 43.102 Å / Origin z: 61.8556 Å
111213212223313233
T0.1599 Å2-0.0151 Å2-0.0139 Å2-0.2215 Å20.0033 Å2--0.1848 Å2
L0.2418 °2-0.1626 °2-0.0155 °2-0.3577 °20.0091 °2--0.2956 °2
S0.0085 Å °-0.0811 Å °-0.0021 Å °0.0457 Å °0.004 Å °-0.0228 Å °-0.0057 Å °-0.0071 Å °-0.007 Å °
Refinement TLS groupSelection details: all

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