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- PDB-6nnn: Xanthomonas citri Dephospho-PGM in complex with glucose-1-phosphate -

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Basic information

Entry
Database: PDB / ID: 6nnn
TitleXanthomonas citri Dephospho-PGM in complex with glucose-1-phosphate
ComponentsPhosphoglucomutase
KeywordsISOMERASE / phosphoglucomutase
Function / homology
Function and homology information


intramolecular phosphotransferase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III ...Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-O-phosphono-alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsStiers, K.M. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1409898 United States
CitationJournal: Struct Dyn. / Year: 2019
Title: Structural and dynamical description of the enzymatic reaction of a phosphohexomutase.
Authors: Stiers, K.M. / Graham, A.C. / Zhu, J.S. / Jakeman, D.L. / Nix, J.C. / Beamer, L.J.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7424
Polymers51,3521
Non-polymers3913
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.730, 54.510, 171.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phosphoglucomutase


Mass: 51351.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: xanA, XAC3579 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PGN7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 22% PEG 8000, 0.2M MgCl, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.35→52 Å / Num. obs: 91307 / % possible obs: 98.3 % / Redundancy: 12.4 % / Biso Wilson estimate: 15.8978765838 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Net I/σ(I): 18.4
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3675 / CC1/2: 0.403 / Rpim(I) all: 0.542 / Rrim(I) all: 1.521 / % possible all: 83.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BMN

5bmn


Resolution: 1.35→51.96 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.8
RfactorNum. reflection% reflection
Rfree0.2028 4555 4.99 %
Rwork0.1743 --
obs0.1757 91231 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→51.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 24 609 4079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063787
X-RAY DIFFRACTIONf_angle_d0.8495162
X-RAY DIFFRACTIONf_dihedral_angle_d7.9472883
X-RAY DIFFRACTIONf_chiral_restr0.081558
X-RAY DIFFRACTIONf_plane_restr0.006698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.49081550.44792872X-RAY DIFFRACTION99
1.3653-1.38140.37911390.36942787X-RAY DIFFRACTION100
1.3814-1.39830.36761610.34822889X-RAY DIFFRACTION100
1.3983-1.4160.33991440.32022817X-RAY DIFFRACTION100
1.416-1.43460.30951620.29862849X-RAY DIFFRACTION100
1.4346-1.45420.30831560.25462861X-RAY DIFFRACTION100
1.4542-1.4750.26891550.24882812X-RAY DIFFRACTION100
1.475-1.4970.24921460.22762878X-RAY DIFFRACTION100
1.497-1.52040.23311460.22042875X-RAY DIFFRACTION100
1.5204-1.54540.24461330.20952848X-RAY DIFFRACTION100
1.5454-1.5720.21361580.20072852X-RAY DIFFRACTION100
1.572-1.60060.23011400.19432876X-RAY DIFFRACTION100
1.6006-1.63140.20951360.18482882X-RAY DIFFRACTION100
1.6314-1.66470.25231700.19042855X-RAY DIFFRACTION100
1.6647-1.70090.22191540.19712864X-RAY DIFFRACTION100
1.7009-1.74050.20211320.19542880X-RAY DIFFRACTION100
1.7405-1.7840.23491540.18952873X-RAY DIFFRACTION100
1.784-1.83220.23841460.18662904X-RAY DIFFRACTION100
1.8322-1.88610.21111440.18692880X-RAY DIFFRACTION100
1.8861-1.9470.21911710.17522876X-RAY DIFFRACTION100
1.947-2.01660.20541570.17492878X-RAY DIFFRACTION100
2.0166-2.09740.18121780.17182875X-RAY DIFFRACTION100
2.0974-2.19280.17791410.15742914X-RAY DIFFRACTION100
2.1928-2.30840.17771690.16632865X-RAY DIFFRACTION100
2.3084-2.45310.19071430.15862926X-RAY DIFFRACTION100
2.4531-2.64250.19921490.16052925X-RAY DIFFRACTION100
2.6425-2.90840.20981760.1672940X-RAY DIFFRACTION100
2.9084-3.32910.191560.15552944X-RAY DIFFRACTION100
3.3291-4.19410.15551470.13733005X-RAY DIFFRACTION100
4.1941-51.99810.16171370.14013174X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 29.7341 Å / Origin y: 51.0703 Å / Origin z: 22.4222 Å
111213212223313233
T0.129 Å2-0.0109 Å20.0147 Å2-0.1322 Å2-0.0203 Å2--0.1402 Å2
L0.255 °2-0.1898 °2-0.0166 °2-0.2814 °20.0454 °2--0.3407 °2
S0.0009 Å °0.0283 Å °-0.0252 Å °-0.0327 Å °0.0056 Å °-0.0009 Å °0.0375 Å °0.0273 Å °-0.0053 Å °
Refinement TLS groupSelection details: all

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