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- PDB-6nol: Xanthomonas citri Dephospho-PGM in complex with mannose-1-phosphate -

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Basic information

Entry
Database: PDB / ID: 6nol
TitleXanthomonas citri Dephospho-PGM in complex with mannose-1-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
1-O-phosphono-alpha-D-mannopyranose / DI(HYDROXYETHYL)ETHER / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 16, 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)51,7424
Polymers51,3521
Non-polymers3913
Water7,945441
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)43.680, 54.720, 173.240
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#4: Sugar ChemComp-M1P / 1-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE 1-PHOSPHATE / 1-O-phosphono-alpha-D-mannose / 1-O-phosphono-D-mannose / 1-O-phosphono-mannose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Manp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
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: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.73→46.262 Å / Num. obs: 44430 / % possible obs: 99.9 % / Redundancy: 11.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.358 / Rpim(I) all: 0.103 / Rrim(I) all: 0.373 / Net I/σ(I): 12.7
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 9.1 % / Rmerge(I) obs: 2.696 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2414 / CC1/2: 0.352 / Rpim(I) all: 0.894 / Rrim(I) all: 2.85 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BMN

5bmn


Resolution: 1.73→46.262 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.58
RfactorNum. reflection% reflection
Rfree0.2488 1999 4.51 %
Rwork0.1905 --
obs0.1931 44291 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→46.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 24 441 3911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073619
X-RAY DIFFRACTIONf_angle_d0.8784916
X-RAY DIFFRACTIONf_dihedral_angle_d4.242942
X-RAY DIFFRACTIONf_chiral_restr0.052537
X-RAY DIFFRACTIONf_plane_restr0.006656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.77330.42991380.43582933X-RAY DIFFRACTION99
1.7733-1.82120.37021420.39552993X-RAY DIFFRACTION99
1.8212-1.87480.36671390.34522935X-RAY DIFFRACTION100
1.8748-1.93530.34191400.28592974X-RAY DIFFRACTION100
1.9353-2.00450.32221410.25782986X-RAY DIFFRACTION100
2.0045-2.08470.25111420.23882994X-RAY DIFFRACTION100
2.0847-2.17960.29121430.22083022X-RAY DIFFRACTION100
2.1796-2.29450.26041400.21382987X-RAY DIFFRACTION100
2.2945-2.43830.26781430.2043006X-RAY DIFFRACTION100
2.4383-2.62650.27881430.19053022X-RAY DIFFRACTION100
2.6265-2.89080.25611430.18863039X-RAY DIFFRACTION100
2.8908-3.3090.24221440.1753048X-RAY DIFFRACTION100
3.309-4.16860.20041470.13793101X-RAY DIFFRACTION100
4.1686-46.27860.18061540.12833252X-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)
10.1487-0.1999-0.03030.33740.1780.2519-0.00460.0172-0.0450.03280.00140.04730.07580.0288-0.00010.16120.01430.01220.1448-0.02290.153739.846237.379515.1134
20.09790.0219-0.03120.0104-0.03090.0839-0.017-0.16140.0223-0.00680.0274-0.04120.08170.0895-0.0010.11830.0147-0.00610.1294-0.00980.122236.138947.293939.5208
30.1678-0.1202-0.12450.2245-0.0590.2457-0.00260.0279-0.0026-0.0112-0.0250.02450.0114-0.0339-00.12110.0008-0.00670.1426-0.00750.134827.303155.980627.4102
40.12880.1013-0.13460.0896-0.11160.13850.0163-0.0752-0.0625-0.0114-0.0535-0.0158-0.01530.0047-0.00010.14170.01420.00840.1242-0.00440.14423.73660.008529.4686
50.0730.0716-0.01710.1023-0.02020.150.00160.0414-0.0444-0.04230.04620.01620.0048-0.0007-00.15270.0045-0.00430.1637-0.02190.168214.215864.094210.0144
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 165:219 )A165 - 219
3X-RAY DIFFRACTION3( CHAIN A AND RESID 220:352 )A220 - 352
4X-RAY DIFFRACTION4( CHAIN A AND RESID 353:399 )A353 - 399
5X-RAY DIFFRACTION5( CHAIN A AND RESID 400:448 )A400 - 448

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