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- PDB-8hnj: Domain-stabilized glutamine-binding protein -

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Basic information

Entry
Database: PDB / ID: 8hnj
TitleDomain-stabilized glutamine-binding protein
ComponentsGlutamine ABC transporter, periplasmic glutamine-binding protein GlnH
KeywordsTRANSPORT PROTEIN / Computationally stabilized / Glutamine-binding protein / Amino acid transport / Domain engineered protein
Function / homology
Function and homology information


amino acid transport / ligand-gated monoatomic ion channel activity / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Glutamine-binding periplasmic protein GlnH, type 2 periplasmic binding protein fold / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / 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.
Similarity search - Domain/homology
GLUTAMINE / Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
Similarity search - Component
Biological speciesEscherichia coli 908519 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsChoi, S.H. / Park, J.H. / Seo, M.H. / Park, K.W. / Lee, W.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Domain-wise dissection of thermal stability enhancement in multidomain proteins.
Authors: Oh, J. / Durai, P. / Kannan, P. / Park, J. / Yeon, Y.J. / Lee, W.K. / Park, K. / Seo, M.H.
History
DepositionDec 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
B: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
C: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
D: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
E: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
F: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,12812
Polymers153,2516
Non-polymers8776
Water9,548530
1
A: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6882
Polymers25,5421
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6882
Polymers25,5421
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6882
Polymers25,5421
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6882
Polymers25,5421
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6882
Polymers25,5421
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6882
Polymers25,5421
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)235.100, 69.590, 83.740
Angle α, β, γ (deg.)90.000, 90.711, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 1 - 218 / Label seq-ID: 1 - 218

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and (resid 1 through 15 or (resid 16...AA
2(chain 'B' and (resid 1 through 15 or (resid 16...BB
3(chain 'C' and (resid 1 through 15 or (resid 16...CC
4(chain 'D' and (resid 1 through 20 or (resid 21...DD
5(chain 'E' and (resid 1 through 15 or (resid 16...EE
6(chain 'F' and (resid 1 through 15 or (resid 16...FF

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Components

#1: Protein
Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH


Mass: 25541.912 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 908519 (bacteria) / Gene: HMPREF1604_05361 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0VBD8
#2: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 200 mM Potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→29.3 Å / Num. obs: 87318 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.94 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→2.03 Å / Num. unique obs: 9517 / CC1/2: 0.692

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→28.79 Å / SU ML: 0.3021 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.0452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 4368 5 %
Rwork0.2259 82950 -
obs0.2278 87318 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.73 Å2
Refinement stepCycle: LAST / Resolution: 2.03→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10052 0 60 530 10642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019210289
X-RAY DIFFRACTIONf_angle_d1.75413913
X-RAY DIFFRACTIONf_chiral_restr0.07451567
X-RAY DIFFRACTIONf_plane_restr0.01151799
X-RAY DIFFRACTIONf_dihedral_angle_d6.66441412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.050.44041470.33872793X-RAY DIFFRACTION99.76
2.05-2.080.3641450.3352742X-RAY DIFFRACTION99.9
2.08-2.10.37791450.3092766X-RAY DIFFRACTION99.97
2.1-2.130.31261440.30032728X-RAY DIFFRACTION99.97
2.13-2.160.30471460.28942785X-RAY DIFFRACTION99.9
2.16-2.190.31211440.29082728X-RAY DIFFRACTION99.86
2.19-2.220.33791450.2862755X-RAY DIFFRACTION99.72
2.22-2.250.33281450.2862749X-RAY DIFFRACTION99.83
2.25-2.290.31861440.28742734X-RAY DIFFRACTION99.9
2.29-2.320.31761490.27752826X-RAY DIFFRACTION99.87
2.32-2.360.31991420.27612702X-RAY DIFFRACTION99.89
2.36-2.410.36151460.2672769X-RAY DIFFRACTION99.93
2.41-2.450.31391460.26642767X-RAY DIFFRACTION99.79
2.45-2.50.31441440.26932742X-RAY DIFFRACTION99.59
2.5-2.560.33511450.25762748X-RAY DIFFRACTION99.86
2.56-2.620.30181460.24872768X-RAY DIFFRACTION99.86
2.62-2.680.29671450.24962759X-RAY DIFFRACTION99.55
2.68-2.750.27511430.2432738X-RAY DIFFRACTION99.59
2.75-2.840.31991450.25062760X-RAY DIFFRACTION99.66
2.84-2.930.31311460.25662770X-RAY DIFFRACTION99.69
2.93-3.030.29411460.23562772X-RAY DIFFRACTION99.52
3.03-3.150.26311450.23962741X-RAY DIFFRACTION99.52
3.15-3.30.24561460.22682784X-RAY DIFFRACTION99.73
3.3-3.470.27921460.21562771X-RAY DIFFRACTION99.45
3.47-3.690.26621450.212761X-RAY DIFFRACTION99.35
3.69-3.970.20921460.19052772X-RAY DIFFRACTION99.45
3.97-4.370.21781470.17822787X-RAY DIFFRACTION99.36
4.37-50.20771460.16522769X-RAY DIFFRACTION98.98
5-6.290.22031480.18942810X-RAY DIFFRACTION99.7
6.29-28.790.18511510.19892854X-RAY DIFFRACTION98.56

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