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- PDB-5bmp: Crystal Structure of Phosphoglucomutase from Xanthomonas citri co... -

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Basic information

Entry
Database: PDB / ID: 5bmp
TitleCrystal Structure of Phosphoglucomutase from Xanthomonas citri complexed with glucose-1-phosphate
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-O-phosphono-alpha-D-glucopyranose / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsGoto, L.S. / Pereira, H.M. / Novo Mansur, M.T.M.
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
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Jul 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 1.5Sep 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 1.6Nov 20, 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)51,5023
Polymers51,2171
Non-polymers2842
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-2 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.861, 54.732, 173.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoglucomutase


Mass: 51217.473 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, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: 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
#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.: 597 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
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/Imidazol 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 23, 2014
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 36037 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.13 % / Rmerge F obs: 1 / Rmerge(I) obs: 0.02 / Rrim(I) all: 0.024 / Χ2: 0.946 / Net I/σ(I): 45.06 / Num. measured all: 132372
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.85-1.960.9970.04122.8914908575151460.0589.5
1.96-2.10.9990.03333.8220708545453960.03898.9
2.1-2.260.9990.02740.0319147506450000.03198.7
2.26-2.480.9990.02445.3318119470346710.02899.3
2.48-2.760.9990.02150.8416570427942510.02499.3
2.76-3.180.9990.01955.6814825380637850.02299.4
3.18-3.870.9990.01962.0512406325832240.02299
3.87-5.370.9990.01764.849863260625710.0298.7
5.3710.01762.885826166815910.01995.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREKdata scaling
XDSdata reduction
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BMN

5bmn


Resolution: 1.85→19.563 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1796 1802 5 %Random selection
Rwork0.152 34235 --
obs0.1534 36037 98.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.63 Å2 / Biso mean: 15.3968 Å2 / Biso min: 4.91 Å2
Refinement stepCycle: final / Resolution: 1.85→19.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 17 597 4069
Biso mean--21.81 27.74 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043545
X-RAY DIFFRACTIONf_angle_d0.8664814
X-RAY DIFFRACTIONf_chiral_restr0.034531
X-RAY DIFFRACTIONf_plane_restr0.005637
X-RAY DIFFRACTIONf_dihedral_angle_d13.0381292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89880.23881210.18632302X-RAY DIFFRACTION87
1.8988-1.95470.2261340.16982553X-RAY DIFFRACTION98
1.9547-2.01770.20781380.16072618X-RAY DIFFRACTION100
2.0177-2.08970.20141390.15582644X-RAY DIFFRACTION100
2.0897-2.17330.19151370.14782608X-RAY DIFFRACTION100
2.1733-2.27210.19321400.1532655X-RAY DIFFRACTION100
2.2721-2.39170.17181380.1562619X-RAY DIFFRACTION100
2.3917-2.54120.16771400.15442662X-RAY DIFFRACTION100
2.5412-2.73690.19381420.15922691X-RAY DIFFRACTION100
2.7369-3.01150.21081390.16132643X-RAY DIFFRACTION99
3.0115-3.44520.18021410.15492694X-RAY DIFFRACTION99
3.4452-4.33280.14861430.12882714X-RAY DIFFRACTION99
4.3328-200.14561500.14392832X-RAY DIFFRACTION99
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)
10.60830.2510.15631.16170.91421.7074-0.0055-0.02890.05620.00110.00630.0284-0.1480.0415-0.00910.0787-0.0125-0.00360.0745-0.01460.0743-3.403216.0771-17.2088
20.45240.04860.20220.72-0.22850.8494-0.0061-0.0310.01080.0105-0.0054-0.01960.01530.00850.00060.0437-0.0023-0.00210.0702-0.01690.0682-15.5649-1.0829-31.3758
30.9152-0.10150.05691.17810.58651.5693-0.0407-0.15670.06330.12370.1284-0.0564-0.00210.0833-0.04120.06970.00210.00270.0809-0.02920.087-29.584-8.1678-10.6976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 181 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 386 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 387 through 470 )A0

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