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- PDB-6noq: Xanthomonas citri Phospho-PGM in complex with mannose-1-phosphate -

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Basic information

Entry
Database: PDB / ID: 6noq
TitleXanthomonas citri Phospho-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 / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.61 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 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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)51,7163
Polymers51,4321
Non-polymers2842
Water9,242513
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)43.700, 54.640, 173.760
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 39.01 %
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: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.61→46.253 Å / Num. obs: 55020 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.311 / Rpim(I) all: 0.092 / Rrim(I) all: 0.324 / Net I/σ(I): 7
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.784 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2656 / CC1/2: 0.348 / Rpim(I) all: 0.652 / Rrim(I) all: 1.904 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.61→46.253 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 27.53
RfactorNum. reflection% reflection
Rfree0.2707 2740 4.99 %
Rwork0.207 --
obs0.2102 54941 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.61→46.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 17 513 3980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063694
X-RAY DIFFRACTIONf_angle_d0.8845032
X-RAY DIFFRACTIONf_dihedral_angle_d6.4832971
X-RAY DIFFRACTIONf_chiral_restr0.052545
X-RAY DIFFRACTIONf_plane_restr0.006678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.63780.48311240.41472558X-RAY DIFFRACTION100
1.6378-1.66760.37781340.34352581X-RAY DIFFRACTION100
1.6676-1.69960.3641230.32312563X-RAY DIFFRACTION100
1.6996-1.73430.36021430.30522575X-RAY DIFFRACTION100
1.7343-1.7720.35351320.28332565X-RAY DIFFRACTION100
1.772-1.81330.351280.26882594X-RAY DIFFRACTION100
1.8133-1.85860.32781500.25292556X-RAY DIFFRACTION100
1.8586-1.90890.29391300.24122608X-RAY DIFFRACTION100
1.9089-1.9650.29451440.22392555X-RAY DIFFRACTION100
1.965-2.02850.28181530.22282568X-RAY DIFFRACTION100
2.0285-2.1010.27571190.20782635X-RAY DIFFRACTION100
2.101-2.18510.26951420.21022616X-RAY DIFFRACTION100
2.1851-2.28450.28611200.21162587X-RAY DIFFRACTION100
2.2845-2.4050.28641380.20982604X-RAY DIFFRACTION100
2.405-2.55560.23741210.19282616X-RAY DIFFRACTION100
2.5556-2.75290.25591280.19842645X-RAY DIFFRACTION100
2.7529-3.02990.28491520.1992632X-RAY DIFFRACTION100
3.0299-3.46820.24881580.17762625X-RAY DIFFRACTION100
3.4682-4.36910.22361490.14592698X-RAY DIFFRACTION100
4.3691-46.27220.18841520.14742820X-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)
10.0219-0.0068-0.00360.01830.00080.0609-0.019-0.0375-0.01470.0148-0.0180.00980.0133-0.0151-0.03380.04470.00030.00020.0657-0.0110.045928.316248.625936.0629
20.0037-0.00110.00570.0046-0.00120.0061-0.0299-0.02010.02040.01260.007-0.02010.0288-0.0412-0.00490.06570.0092-0.00130.0787-0.04370.092133.19763.072121.5004
30.00150.0075-0.00560.0114-0.00920.0058-0.0279-0.0121-0.00840.0057-0.0264-0.03160.01480.0189-0.02080.057-0.0060.00510.0528-0.02530.044923.601359.825829.5259
40.00510.00540.00120.02860.00260.0028-0.0193-0.00980.0193-0.02290.0301-0.00310.01380.00220.00170.0421-0.0182-0.0280.0485-0.08640.101713.864463.792810.1221
50.0072-0.01450.00640.02840.01090.04140.0123-0.00980.0079-0.0120.0402-0.03360.00570.02150.05620.0794-0.00620.01540.066-0.04410.073239.858537.321514.9604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 143:267 )A143 - 267
2X-RAY DIFFRACTION2( CHAIN A AND RESID 268:330 )A268 - 330
3X-RAY DIFFRACTION3( CHAIN A AND RESID 331:377 )A331 - 377
4X-RAY DIFFRACTION4( CHAIN A AND RESID 378:448 )A378 - 448
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1:142 )A1 - 142

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