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- PDB-6nnt: Xanthomonas citri Dephospho-PGM in complex with glucose-1,6-bisph... -

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Basic information

Entry
Database: PDB / ID: 6nnt
TitleXanthomonas citri Dephospho-PGM in complex with glucose-1,6-bisphosphate
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, 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, 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, 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / 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
1,6-di-O-phosphono-alpha-D-glucopyranose / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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: Data collection / Database references ...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
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)51,7153
Polymers51,3521
Non-polymers3632
Water11,422634
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)43.620, 54.740, 173.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Sugar ChemComp-G16 / 1,6-di-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE / 1,6-di-O-phosphono-alpha-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose


Type: D-saccharide / Mass: 339.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O12P2
IdentifierTypeProgram
a-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
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: 1.45→52.2 Å / Num. obs: 74685 / % possible obs: 100 % / Redundancy: 14.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.03 / Rrim(I) all: 0.118 / Net I/σ(I): 17.1
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.421 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3597 / CC1/2: 0.429 / Rpim(I) all: 0.807 / Rrim(I) all: 2.559 / % possible all: 99.3

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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: 1.45→52.198 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 19.31
RfactorNum. reflection% reflection
Rfree0.2078 3838 5.14 %
Rwork0.1689 --
obs0.1709 74627 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→52.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 21 634 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063737
X-RAY DIFFRACTIONf_angle_d0.9085105
X-RAY DIFFRACTIONf_dihedral_angle_d8.4332140
X-RAY DIFFRACTIONf_chiral_restr0.095560
X-RAY DIFFRACTIONf_plane_restr0.006684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46840.3021390.31292560X-RAY DIFFRACTION100
1.4684-1.48770.34871360.30392608X-RAY DIFFRACTION100
1.4877-1.50810.31811290.28022585X-RAY DIFFRACTION100
1.5081-1.52960.25421400.25342573X-RAY DIFFRACTION100
1.5296-1.55240.26351620.22192597X-RAY DIFFRACTION100
1.5524-1.57670.26291520.22122554X-RAY DIFFRACTION100
1.5767-1.60260.2351520.19872574X-RAY DIFFRACTION100
1.6026-1.63020.23051560.20042583X-RAY DIFFRACTION100
1.6302-1.65980.2161280.19692611X-RAY DIFFRACTION100
1.6598-1.69180.22691360.19482570X-RAY DIFFRACTION100
1.6918-1.72630.23441440.19682591X-RAY DIFFRACTION100
1.7263-1.76380.24211560.19272606X-RAY DIFFRACTION100
1.7638-1.80490.24251410.1872582X-RAY DIFFRACTION100
1.8049-1.850.26721250.20072624X-RAY DIFFRACTION100
1.85-1.90.23261500.18962633X-RAY DIFFRACTION100
1.9-1.95590.23181400.17662593X-RAY DIFFRACTION100
1.9559-2.01910.18691390.17192607X-RAY DIFFRACTION100
2.0191-2.09120.1941200.16412636X-RAY DIFFRACTION100
2.0912-2.1750.22071510.15792618X-RAY DIFFRACTION100
2.175-2.2740.211420.17022625X-RAY DIFFRACTION100
2.274-2.39380.20971300.16182651X-RAY DIFFRACTION100
2.3938-2.54380.21521640.16222601X-RAY DIFFRACTION100
2.5438-2.74020.20331460.16072667X-RAY DIFFRACTION100
2.7402-3.0160.17541250.16392668X-RAY DIFFRACTION100
3.016-3.45230.19161420.14782685X-RAY DIFFRACTION100
3.4523-4.34920.17331380.12622738X-RAY DIFFRACTION100
4.3492-52.23150.16621550.14232849X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4227-0.0818-0.0180.75970.55410.925-0.01960.0085-0.0175-0.00910.01560.02170.11040.0866-0.00740.08480.01350.00390.0797-0.01620.078141.698339.308119.6132
20.1634-0.16950.08590.329-0.19120.37710.00330.0245-0.0208-0.0246-0.01170.01440.0030.0111-0.00280.0802-0.00370.00530.0895-0.01590.092223.67457.55325.0012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:164 )A23 - 164
2X-RAY DIFFRACTION2( CHAIN A AND RESID 165:448 )A165 - 448

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