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- PDB-7nss: Bdellovibrio bacteriovorus PGI in P3121 spacegroup -

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Basic information

Entry
Database: PDB / ID: 7nss
TitleBdellovibrio bacteriovorus PGI in P3121 spacegroup
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Glucose-6-phosphate isomerase Isomerase Phosphoglucose isomerase
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMeek, R.W. / Lovering, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)1360362 United Kingdom
CitationJournal: Open Biology / Year: 2021
Title: Bdellovibrio bacteriovorus phosphoglucose isomerase structures reveal novel rigidity in the active site of a selected subset of enzymes upon substrate binding.
Authors: Meek, R.W. / Cadby, I.T. / Lovering, A.L.
History
DepositionMar 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1172
Polymers48,0551
Non-polymers621
Water4,486249
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2354
Polymers96,1112
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10210 Å2
ΔGint-50 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.030, 101.030, 76.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Glucose-6-phosphate isomerase /


Mass: 48055.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: pgi, Bd0741 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MPU9, glucose-6-phosphate isomerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate pH 5.0 and 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→57.74 Å / Num. obs: 37920 / % possible obs: 95.8 % / Redundancy: 18.7 % / Biso Wilson estimate: 28.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.034 / Rrim(I) all: 0.106 / Net I/σ(I): 23.2
Reflection shellResolution: 1.84→1.87 Å / Rmerge(I) obs: 1.919 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2876 / CC1/2: 0.559 / Rpim(I) all: 0.821

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b0z

1b0z


Resolution: 1.84→57.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 1859 4.9 %RANDOM
Rwork0.1892 ---
obs0.1908 36033 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.86 Å2 / Biso mean: 35.017 Å2 / Biso min: 21.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: final / Resolution: 1.84→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 4 249 3433
Biso mean--50.84 40.84 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133254
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173176
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.6324388
X-RAY DIFFRACTIONr_angle_other_deg2.2731.5787329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.915407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0323.077156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52415614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6611517
X-RAY DIFFRACTIONr_chiral_restr0.0730.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023622
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02720
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 143 -
Rwork0.357 2728 -
all-2871 -
obs--99.79 %

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