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- PDB-6nnu: Xanthomonas citri Phospho-PGM in complex with glucose-1,6-phosphate -

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Basic information

Entry
Database: PDB / ID: 6nnu
TitleXanthomonas citri Phospho-PGM in complex with glucose-1,6-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, 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 / DI(HYDROXYETHYL)ETHER / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)51,9174
Polymers51,4321
Non-polymers4853
Water13,601755
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)43.690, 54.720, 173.690
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: 51431.621 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 277 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: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.46→46.3 Å / Num. obs: 73467 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.041 / Rrim(I) all: 0.151 / Net I/σ(I): 14.4
Reflection shellResolution: 1.46→1.48 Å / Redundancy: 8.8 % / Rmerge(I) obs: 2.15 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3579 / CC1/2: 0.345 / Rpim(I) all: 0.759 / Rrim(I) all: 2.286 / % possible all: 100

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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: 1.46→46.296 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 19.19
RfactorNum. reflection% reflection
Rfree0.2071 3666 5 %
Rwork0.1691 --
obs0.1711 73378 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→46.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 28 755 4233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053752
X-RAY DIFFRACTIONf_angle_d0.8485116
X-RAY DIFFRACTIONf_dihedral_angle_d6.6112139
X-RAY DIFFRACTIONf_chiral_restr0.08553
X-RAY DIFFRACTIONf_plane_restr0.006690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.47920.33421330.31872630X-RAY DIFFRACTION100
1.4792-1.49950.32431510.29872614X-RAY DIFFRACTION100
1.4995-1.52090.34561180.2762710X-RAY DIFFRACTION100
1.5209-1.54360.28411270.24342606X-RAY DIFFRACTION100
1.5436-1.56770.23741460.22452666X-RAY DIFFRACTION100
1.5677-1.59340.25321410.20692628X-RAY DIFFRACTION100
1.5934-1.62090.23941350.20472662X-RAY DIFFRACTION100
1.6209-1.65040.23381390.19192618X-RAY DIFFRACTION100
1.6504-1.68210.22141350.19282692X-RAY DIFFRACTION100
1.6821-1.71650.2181300.19542654X-RAY DIFFRACTION100
1.7165-1.75380.22721440.19382694X-RAY DIFFRACTION100
1.7538-1.79460.23381370.1842613X-RAY DIFFRACTION100
1.7946-1.83950.24691340.18662690X-RAY DIFFRACTION100
1.8395-1.88920.20211450.1892665X-RAY DIFFRACTION100
1.8892-1.94480.2331320.1752664X-RAY DIFFRACTION100
1.9448-2.00760.22361400.17242657X-RAY DIFFRACTION100
2.0076-2.07930.20561340.17112686X-RAY DIFFRACTION100
2.0793-2.16260.18721550.16062649X-RAY DIFFRACTION100
2.1626-2.2610.21211400.16482690X-RAY DIFFRACTION100
2.261-2.38020.23351280.16312710X-RAY DIFFRACTION100
2.3802-2.52930.20551530.16072678X-RAY DIFFRACTION100
2.5293-2.72460.21510.16562720X-RAY DIFFRACTION100
2.7246-2.99870.20171290.16772719X-RAY DIFFRACTION100
2.9987-3.43250.19571690.152715X-RAY DIFFRACTION100
3.4325-4.32410.15961700.12512760X-RAY DIFFRACTION100
4.3241-46.31960.1761500.13872922X-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)
10.2854-0.1509-0.32640.3180.33140.5467-0.0296-0.0107-0.0284-0.02260.0196-0.00710.04230.0283-0.00110.09730.0038-0.00380.0874-0.01110.08838.572540.415522.0103
20.0665-0.078-0.07230.2912-0.10710.4376-0.01210.0207-0.0051-0.0048-0.0031-0.0193-0.0124-0.0055-00.0818-0.0023-0.00110.1081-0.01280.099127.481156.137627.2007
30.1688-0.1429-0.0580.1266-0.13040.1338-0.01530.0063-0.0394-0.02360.00870.0031-0.02110.0255-00.0992-0.00310.00190.0805-0.00950.101123.855459.902429.45
40.23330.17810.10340.2694-0.13870.3657-0.00840.0744-0.066-0.08270.0411-0.0467-0.00760.01130.09950.115-0.0049-0.00520.1102-0.02970.126514.029163.601610.2137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 197 )
2X-RAY DIFFRACTION2chain 'A' and (resid 198 through 330 )
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 377 )
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 448 )

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