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

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Basic information

Entry
Database: PDB / ID: 6nnp
TitleXanthomonas citri Dephospho-PGM in complex with glucose-6-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
6-O-phosphono-alpha-D-glucopyranose / PHOSPHATE ION / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 / _chem_comp.type / _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

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Assembly

Deposited unit
A: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7314
Polymers51,3521
Non-polymers3793
Water9,566531
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)43.780, 54.590, 171.810
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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 Å3/Da / Density % sol: 38.47 %
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: 1.5→52.027 Å / Num. obs: 67042 / % possible obs: 94.4 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.024 / Rrim(I) all: 0.081 / Net I/σ(I): 17.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.854 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2681 / CC1/2: 0.457 / Rpim(I) all: 0.672 / Rrim(I) all: 1.981 / % possible all: 81.8

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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: 1.5→52.027 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.47
RfactorNum. reflection% reflection
Rfree0.2112 3317 4.95 %
Rwork0.1782 --
obs0.1798 67030 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→52.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 22 531 3999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063742
X-RAY DIFFRACTIONf_angle_d0.895103
X-RAY DIFFRACTIONf_dihedral_angle_d14.8572246
X-RAY DIFFRACTIONf_chiral_restr0.054551
X-RAY DIFFRACTIONf_plane_restr0.006689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52150.31211290.31292654X-RAY DIFFRACTION100
1.5215-1.54420.33331640.30782552X-RAY DIFFRACTION100
1.5442-1.56830.32331600.28872634X-RAY DIFFRACTION100
1.5683-1.5940.29051340.27222589X-RAY DIFFRACTION100
1.594-1.62150.32611500.27422610X-RAY DIFFRACTION100
1.6215-1.6510.31471390.26632598X-RAY DIFFRACTION100
1.651-1.68270.28071410.25312621X-RAY DIFFRACTION100
1.6827-1.71710.30881250.26282641X-RAY DIFFRACTION100
1.7171-1.75440.2911480.24232639X-RAY DIFFRACTION100
1.7544-1.79520.30571310.23792600X-RAY DIFFRACTION100
1.7952-1.84010.24561310.21972671X-RAY DIFFRACTION100
1.8401-1.88990.24221190.21272647X-RAY DIFFRACTION100
1.8899-1.94550.22761230.20562647X-RAY DIFFRACTION100
1.9455-2.00830.26281450.18292607X-RAY DIFFRACTION100
2.0083-2.08010.19921470.17752632X-RAY DIFFRACTION100
2.0801-2.16340.19461260.1652659X-RAY DIFFRACTION100
2.1634-2.26180.1871180.17262688X-RAY DIFFRACTION100
2.2618-2.38110.19631350.16612643X-RAY DIFFRACTION100
2.3811-2.53030.22081350.16842665X-RAY DIFFRACTION100
2.5303-2.72560.19831450.16112698X-RAY DIFFRACTION100
2.7256-2.99990.21461340.16692670X-RAY DIFFRACTION100
2.9999-3.43390.21121420.15552721X-RAY DIFFRACTION100
3.4339-4.3260.13881430.13442749X-RAY DIFFRACTION100
4.326-52.05820.16551530.14392878X-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)
10.6632-0.3791-0.19351.39790.51451.2175-0.01410.0463-0.0426-0.0777-0.00360.10740.10730.00060.01530.17940.00930.01060.1687-0.02610.163439.443537.599615.0069
20.1508-0.22750.07470.5462-0.24420.8722-0.00870.02530.0067-0.0056-0.0124-0.0452-0.00080.03850.02150.1212-0.00220.00730.1502-0.01140.150428.793554.985830.0105
31.13430.1444-0.12971.03510.30811.2554-0.06670.185-0.1204-0.08340.04630.01590.0023-0.05170.01690.165-0.00520.00140.1651-0.02020.163614.38163.94979.972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 377 )
3X-RAY DIFFRACTION3chain 'A' and (resid 378 through 448 )

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