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- PDB-6h1u: GlnH bound to Asp, Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6h1u
TitleGlnH bound to Asp, Mycobacterium tuberculosis
ComponentsProbable glutamine-binding lipoprotein GlnH (GLNBP)
KeywordsSIGNALING PROTEIN / Solute-binding protein / amino acid binding / transport / serine threonine protein kinase
Function / homology: / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / outer membrane-bounded periplasmic space / Prokaryotic membrane lipoprotein lipid attachment site profile. / extracellular region / ASPARTIC ACID / Probable glutamine-binding lipoprotein GlnH (GLNBP)
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsO'Hare, H.M. / Wallis, R. / Lin, L.Y. / Newland-Smith, Z.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_PC_16051 United Kingdom
CitationJournal: MBio / Year: 2018
Title: An Aspartate-Specific Solute-Binding Protein Regulates Protein Kinase G Activity To Control Glutamate Metabolism in Mycobacteria.
Authors: Bhattacharyya, N. / Nkumama, I.N. / Newland-Smith, Z. / Lin, L.Y. / Yin, W. / Cullen, R.E. / Griffiths, J.S. / Jarvis, A.R. / Price, M.J. / Chong, P.Y. / Wallis, R. / O'Hare, H.M.
History
DepositionJul 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable glutamine-binding lipoprotein GlnH (GLNBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4462
Polymers31,3131
Non-polymers1331
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.980, 81.880, 88.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable glutamine-binding lipoprotein GlnH (GLNBP)


Mass: 31312.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: glnH, Rv0411c / Production host: Escherichia coli (E. coli) / References: UniProt: P96257
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH6, 0.2M MgCl2, 20% PEG 6000, 10 mM sodium aspartate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.68→59.93 Å / Num. obs: 41100 / % possible obs: 99.95 % / Redundancy: 5.9 % / Biso Wilson estimate: 20.12 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.029 / Rrim(I) all: 0.071 / Net I/σ(I): 16.3
Reflection shellResolution: 1.68→1.71 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2722refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v25

2v25


Resolution: 1.68→42.801 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.46
RfactorNum. reflection% reflection
Rfree0.1978 1988 4.84 %
Rwork0.1725 --
obs0.1737 41074 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.36 Å2 / Biso mean: 25.1345 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 1.68→42.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 9 267 2476
Biso mean--16.65 48.13 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072264
X-RAY DIFFRACTIONf_angle_d0.8483101
X-RAY DIFFRACTIONf_chiral_restr0.06367
X-RAY DIFFRACTIONf_plane_restr0.006410
X-RAY DIFFRACTIONf_dihedral_angle_d5.1491925
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.68-1.7220.28141410.236327132854
1.722-1.76860.28881520.212127582910
1.7686-1.82060.21771390.193327502889
1.8206-1.87940.21341530.18427532906
1.8794-1.94660.20211260.183327702896
1.9466-2.02450.18881340.165827542888
2.0245-2.11660.18961470.170427622909
2.1166-2.22820.20191380.172627882926
2.2282-2.36780.21251270.176227872914
2.3678-2.55060.20661640.168627752939
2.5506-2.80730.18861550.173427892944
2.8073-3.21330.19211510.16628042955
3.2133-4.0480.19951280.153628813009
4.048-42.81470.17281330.177230023135
Refinement TLS params.Method: refined / Origin x: -17.5669 Å / Origin y: -13.5845 Å / Origin z: 13.7135 Å
111213212223313233
T0.0913 Å2-0.0232 Å20.0127 Å2-0.1063 Å2-0.0134 Å2--0.0756 Å2
L1.0589 °2-0.8231 °2-0.0594 °2-1.7965 °2-0.0088 °2--0.6828 °2
S-0.008 Å °-0.0512 Å °0.0034 Å °0.0055 Å °0.0174 Å °-0.0235 Å °-0.0395 Å °0.041 Å °-0.01 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA42 - 328
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 318

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