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- PDB-8v2t: Phosphoheptose isomerase GMHA from Burkholderia pseudomallei boun... -

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Basic information

Entry
Database: PDB / ID: 8v2t
TitlePhosphoheptose isomerase GMHA from Burkholderia pseudomallei bound to inhibitor Mut148591
ComponentsPhosphoheptose isomerase
KeywordsISOMERASE/INHIBITOR / heptose biosynthesis / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


D-sedoheptulose-7-phosphate isomerase / D-sedoheptulose 7-phosphate isomerase activity / D-glycero-D-manno-heptose 7-phosphate biosynthetic process / capsule polysaccharide biosynthetic process / carbohydrate derivative binding / zinc ion binding / cytoplasm
Similarity search - Function
Phosphoheptose isomerase / GmhA/DiaA / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily
Similarity search - Domain/homology
Chem-XLR / Phosphoheptose isomerase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1106a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 Å
AuthorsJunop, M.S. / Brown, C. / Szabla, R.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-89903 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-05980 Canada
CitationJournal: J.Med.Chem. / Year: 2024
Title: Potentiating Activity of GmhA Inhibitors on Gram-Negative Bacteria.
Authors: Moreau, F. / Atamanyuk, D. / Blaukopf, M. / Barath, M. / Herczeg, M. / Xavier, N.M. / Monbrun, J. / Airiau, E. / Henryon, V. / Leroy, F. / Floquet, S. / Bonnard, D. / Szabla, R. / Brown, C. ...Authors: Moreau, F. / Atamanyuk, D. / Blaukopf, M. / Barath, M. / Herczeg, M. / Xavier, N.M. / Monbrun, J. / Airiau, E. / Henryon, V. / Leroy, F. / Floquet, S. / Bonnard, D. / Szabla, R. / Brown, C. / Junop, M.S. / Kosma, P. / Gerusz, V.
History
DepositionNov 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 2.0Dec 13, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Refinement description
Category: atom_site / pdbx_database_related ...atom_site / pdbx_database_related / pdbx_entity_instance_feature / refine / refine_ls_shell
Item: _atom_site.B_iso_or_equiv / _atom_site.occupancy ..._atom_site.B_iso_or_equiv / _atom_site.occupancy / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work
Description: Atoms with unrealistic or zero occupancies / Details: Updated occupancy of Zn metal ion from 1.0 to 0.6 / Provider: author / Type: Coordinate replacement
Revision 2.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2May 1, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8275
Polymers23,3941
Non-polymers4334
Water3,927218
1
A: Phosphoheptose isomerase
hetero molecules

A: Phosphoheptose isomerase
hetero molecules

A: Phosphoheptose isomerase
hetero molecules

A: Phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,30620
Polymers93,5744
Non-polymers1,73216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area14500 Å2
ΔGint-274 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.906, 60.906, 92.728
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-203-

CL

21A-301-

HOH

31A-463-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoheptose isomerase


Mass: 23393.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1106a (bacteria)
Strain: K96423 / Gene: gmhA / Plasmid: pNIC28-Bsa4
Details (production host): gmhA gene cloned into pNIC28-Bsa4 plasmid backbone
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93UJ2

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Non-polymers , 5 types, 222 molecules

#2: Chemical ChemComp-XLR / 1,5,6-trideoxy-6,6-difluoro-1-(N-hydroxyformamido)-6-phosphono-D-ribo-hexitol


Mass: 309.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14F2NO8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.75 Å3/Da / Density % sol: 33.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1 uL protein solution (10 mg/mL GmhA, 500 mM sodium chloride, 10 mM HEPES, pH 7.0) + crystallization solution (10% w/v PEG4000, 0.1 M sodium acetate, pH 4.6) suspended over 1.5 M ammonium ...Details: 1 uL protein solution (10 mg/mL GmhA, 500 mM sodium chloride, 10 mM HEPES, pH 7.0) + crystallization solution (10% w/v PEG4000, 0.1 M sodium acetate, pH 4.6) suspended over 1.5 M ammonium sulfate. Once crystals were grown, 0.2 uL ligand solution (50 mM Mut148591, 50 mM HEPES, pH 7.5) was added to the drops and allowed to soak for 90 minutes.
Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen cryo-stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.402→39.06 Å / Num. obs: 34849 / % possible obs: 99.64 % / Redundancy: 12 % / Biso Wilson estimate: 13.42 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06467 / Rpim(I) all: 0.01944 / Rrim(I) all: 0.06761 / Net I/σ(I): 21.23
Reflection shellResolution: 1.402→1.452 Å / Redundancy: 10 % / Rmerge(I) obs: 0.4377 / Mean I/σ(I) obs: 3.22 / Num. unique obs: 3323 / CC1/2: 0.946 / CC star: 0.986 / Rpim(I) all: 0.1396 / Rrim(I) all: 0.4607 / % possible all: 96.54

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC1.0.5 (20221121)data processing
XDSJan 10, 2022 (BUILT 20220220)data reduction
pointless1.12.12data scaling
Aimless0.7.7data scaling
PHASER1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2X3Y

2x3y


Resolution: 1.402→39.06 Å / SU ML: 0.1263 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.7947
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1631 1745 5.01 %
Rwork0.1566 33101 -
obs0.1569 34846 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.5 Å2
Refinement stepCycle: LAST / Resolution: 1.402→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 22 218 1635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821446
X-RAY DIFFRACTIONf_angle_d0.96421960
X-RAY DIFFRACTIONf_chiral_restr0.0665228
X-RAY DIFFRACTIONf_plane_restr0.0283256
X-RAY DIFFRACTIONf_dihedral_angle_d14.0467517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.402-1.440.26481420.26252595X-RAY DIFFRACTION95.87
1.44-1.490.22171320.19372722X-RAY DIFFRACTION99.96
1.49-1.540.19671500.16832720X-RAY DIFFRACTION100
1.54-1.60.16581470.17182722X-RAY DIFFRACTION99.97
1.6-1.680.18621450.16932714X-RAY DIFFRACTION99.97
1.68-1.770.17461220.17142759X-RAY DIFFRACTION100
1.77-1.880.16561560.16472735X-RAY DIFFRACTION100
1.88-2.020.1681470.14942750X-RAY DIFFRACTION100
2.02-2.230.13841380.13982783X-RAY DIFFRACTION100
2.23-2.550.12941480.13672793X-RAY DIFFRACTION100
2.55-3.210.17321550.15152818X-RAY DIFFRACTION100
3.21-39.060.1561630.15452990X-RAY DIFFRACTION100

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