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- PDB-5eyf: Crystal Structure of Solute-binding Protein from Enterococcus fae... -

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Basic information

Entry
Database: PDB / ID: 5eyf
TitleCrystal Structure of Solute-binding Protein from Enterococcus faecium with Bound Glutamate
ComponentsGlutamate ABC superfamily ATP binding cassette transporter, binding protein
Keywordssolute-binding protein / alpha beta fold / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / membrane / metal ion binding
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate ABC superfamily ATP binding cassette transporter, binding protein
Similarity search - Component
Biological speciesEnterococcus faecium DO (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsMaltseva, N. / Kim, Y. / Mulligan, R. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of Solute-binding Protein from Enterococcus faecium with Bound Glutamate
Authors: Maltseva, N. / Kim, Y. / Mulligan, R. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 2.0Feb 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,8699
Polymers54,4312
Non-polymers4387
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-42 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.405, 115.434, 53.825
Angle α, β, γ (deg.)90.00, 101.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamate ABC superfamily ATP binding cassette transporter, binding protein / solute-binding protein


Mass: 27215.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium DO (bacteria) / Strain: DO / Gene: glnH, HMPREF0351_11286 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q3XZW5
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H9NO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000; 0.1M Tris-HCl pH 8.5; 0.2 M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 66736 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rsym value: 0.074 / Net I/σ(I): 23.6
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→31.569 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.181 3346 5.02 %
Rwork0.1463 --
obs0.148 66598 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→31.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3751 0 25 378 4154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094148
X-RAY DIFFRACTIONf_angle_d1.0565645
X-RAY DIFFRACTIONf_dihedral_angle_d14.9692544
X-RAY DIFFRACTIONf_chiral_restr0.062634
X-RAY DIFFRACTIONf_plane_restr0.007763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.54170.20921550.16712612X-RAY DIFFRACTION100
1.5417-1.56470.22271510.15142580X-RAY DIFFRACTION100
1.5647-1.58920.19911500.14742697X-RAY DIFFRACTION100
1.5892-1.61520.21991400.14482566X-RAY DIFFRACTION100
1.6152-1.64310.18851400.14052623X-RAY DIFFRACTION100
1.6431-1.6730.1981350.14032656X-RAY DIFFRACTION100
1.673-1.70510.21221420.14272611X-RAY DIFFRACTION100
1.7051-1.73990.20121420.13662661X-RAY DIFFRACTION100
1.7399-1.77780.18121310.12712614X-RAY DIFFRACTION100
1.7778-1.81910.16731380.12612671X-RAY DIFFRACTION100
1.8191-1.86460.18931310.12522604X-RAY DIFFRACTION100
1.8646-1.9150.2111290.13692660X-RAY DIFFRACTION100
1.915-1.97140.19011330.13572593X-RAY DIFFRACTION100
1.9714-2.0350.16991280.12912686X-RAY DIFFRACTION100
2.035-2.10770.17251420.12882617X-RAY DIFFRACTION100
2.1077-2.19210.17711600.13312602X-RAY DIFFRACTION100
2.1921-2.29180.1891530.14022643X-RAY DIFFRACTION100
2.2918-2.41260.21731170.14742668X-RAY DIFFRACTION100
2.4126-2.56370.18391230.15362654X-RAY DIFFRACTION100
2.5637-2.76150.18451290.1682652X-RAY DIFFRACTION100
2.7615-3.03920.18481340.16992651X-RAY DIFFRACTION100
3.0392-3.47850.1791490.15222620X-RAY DIFFRACTION100
3.4785-4.38070.13871650.13732630X-RAY DIFFRACTION100
4.3807-31.57580.19851290.15582681X-RAY DIFFRACTION99

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