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- PDB-5kl0: Crystal Structure of Phosphoglucomutase from Xanthomonas citri ci... -

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Basic information

Entry
Database: PDB / ID: 5kl0
TitleCrystal Structure of Phosphoglucomutase from Xanthomonas citri citri complexed with Glucose-1,6-biphosphate
ComponentsPhosphoglucomutase
KeywordsISOMERASE / Phosphoglucomutase citrus canker
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.853 Å
AuthorsGoto, L.S. / Pereira, H.M. / Novo Mansur, M.T.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
CAPES23038.006942/2011-31 Brazil
Sao Paulo Research Foundation (FAPESP)2007/50910-2 Brazil
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Structural and functional characterization of the phosphoglucomutase from Xanthomonas citri subsp. citri.
Authors: Goto, L.S. / Vessoni Alexandrino, A. / Malvessi Pereira, C. / Silva Martins, C. / D'Muniz Pereira, H. / Brandao-Neto, J. / Marques Novo-Mansur, M.T.
History
DepositionJun 23, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJul 13, 2016ID: 5BMR
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 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 1.6Sep 27, 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 1.7Nov 6, 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)51,4433
Polymers51,0791
Non-polymers3632
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.980, 54.788, 173.495
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: 51079.328 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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / 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.: 507 / 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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5 % PEG 1000, 12.5 % PEG 3350, 12.5 % MPD, 30 mM MgCl2, 30 mM CaCl2, 100 mM MES/Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 24, 2014 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→19.613 Å / Num. obs: 35635 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.71 % / Biso Wilson estimate: 14.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02 / Net I/σ(I): 45.06
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.85-1.960.04122.89189.5
1.96-2.10.03333.82198.9
2.1-2.260.02740.03198.7
2.26-2.480.02445.33199.3
2.48-2.760.02150.84199.3
2.76-3.180.01955.68199.4
3.18-3.870.01962.05199
3.87-5.370.01764.84198.7
5.37-19.6130.01762.88195.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
d*TREKdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BMN

5bmn


Resolution: 1.853→19.613 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 1782 5 %Random Selection
Rwork0.1455 ---
obs0.1475 35633 97.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.853→19.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 21 507 3978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083544
X-RAY DIFFRACTIONf_angle_d0.8934814
X-RAY DIFFRACTIONf_dihedral_angle_d13.2522108
X-RAY DIFFRACTIONf_chiral_restr0.059530
X-RAY DIFFRACTIONf_plane_restr0.006636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.853-1.90310.19981160.16012211X-RAY DIFFRACTION84
1.9031-1.95910.21541300.15142464X-RAY DIFFRACTION94
1.9591-2.02220.1931360.14272594X-RAY DIFFRACTION99
2.0222-2.09440.17791380.14082617X-RAY DIFFRACTION99
2.0944-2.17820.18171360.13432584X-RAY DIFFRACTION99
2.1782-2.27720.18481380.13962610X-RAY DIFFRACTION99
2.2772-2.3970.21181370.14642612X-RAY DIFFRACTION99
2.397-2.54690.18511390.1482649X-RAY DIFFRACTION100
2.5469-2.74310.18321410.15542668X-RAY DIFFRACTION99
2.7431-3.01820.21531390.15972645X-RAY DIFFRACTION99
3.0182-3.45290.20561420.15612690X-RAY DIFFRACTION99
3.4529-4.34250.15541410.12872693X-RAY DIFFRACTION99
4.3425-19.61440.16541490.1442814X-RAY DIFFRACTION98
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)
10.7752-0.0266-0.14391.48341.18382.2893-0.040.0753-0.0864-0.05390.01090.04640.17450.07570.03730.09540.02270.00680.1115-0.03180.1068-3.334-16.233817.4241
20.46520.0069-0.19680.8153-0.26341.0936-0.01040.0224-0.0065-0.0092-0.0052-0.0228-0.02560.00910.01720.04090.00390.00410.0793-0.01770.0782-15.01370.112731.2239
30.85850.25260.62920.6937-0.18392.2060.01450.1597-0.1042-0.11980.09320.0030.07360.0486-0.03310.0870.0062-0.00060.0788-0.02680.1104-28.9858.6514.353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 372 )
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 470 )

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