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- PDB-6nns: Xanthomonas citri Phospho-PGM in complex with glucose-6-phosphate -

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Basic information

Entry
Database: PDB / ID: 6nns
TitleXanthomonas citri Phospho-PGM in complex with glucose-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, 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
6-O-phosphono-alpha-D-glucopyranose / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 / _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
Revision 1.5Oct 23, 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)51,7323
Polymers51,4321
Non-polymers3002
Water11,656647
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)43.720, 54.520, 172.480
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-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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 Å3/Da / Density % sol: 38.45 %
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: 1.45→46.08 Å / Num. obs: 73075 / % possible obs: 98.4 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.035 / Rrim(I) all: 0.122 / Net I/σ(I): 16.4
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.724 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3033 / CC1/2: 0.367 / Rpim(I) all: 0.802 / Rrim(I) all: 1.912 / % possible all: 84.2

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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: 1.45→39.561 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.57
RfactorNum. reflection% reflection
Rfree0.2104 3692 4.98 %
Rwork0.1782 --
obs0.1799 74113 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→39.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 17 647 4114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063547
X-RAY DIFFRACTIONf_angle_d0.8444818
X-RAY DIFFRACTIONf_dihedral_angle_d7.6582093
X-RAY DIFFRACTIONf_chiral_restr0.079531
X-RAY DIFFRACTIONf_plane_restr0.006638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46910.51521240.45452663X-RAY DIFFRACTION99
1.4691-1.48920.39241460.4052649X-RAY DIFFRACTION99
1.4892-1.51050.36811320.3452686X-RAY DIFFRACTION100
1.5105-1.5330.36121230.29892642X-RAY DIFFRACTION100
1.533-1.5570.28931460.25762720X-RAY DIFFRACTION100
1.557-1.58250.27821340.23242641X-RAY DIFFRACTION100
1.5825-1.60980.24911550.20792681X-RAY DIFFRACTION100
1.6098-1.63910.25081210.19912663X-RAY DIFFRACTION100
1.6391-1.67060.21451500.1882691X-RAY DIFFRACTION100
1.6706-1.70470.19461290.1812721X-RAY DIFFRACTION100
1.7047-1.74180.23091390.17642668X-RAY DIFFRACTION100
1.7418-1.78230.20321380.17932672X-RAY DIFFRACTION100
1.7823-1.82690.23061360.18412713X-RAY DIFFRACTION100
1.8269-1.87620.20161480.18832685X-RAY DIFFRACTION100
1.8762-1.93150.22471380.18372692X-RAY DIFFRACTION100
1.9315-1.99380.2281370.17672713X-RAY DIFFRACTION100
1.9938-2.06510.18491380.17342700X-RAY DIFFRACTION100
2.0651-2.14770.20061590.16852675X-RAY DIFFRACTION100
2.1477-2.24550.2341380.16942723X-RAY DIFFRACTION100
2.2455-2.36380.23271280.16992726X-RAY DIFFRACTION100
2.3638-2.51190.21171580.16592733X-RAY DIFFRACTION100
2.5119-2.70580.21171520.16872722X-RAY DIFFRACTION100
2.7058-2.9780.18271300.17742743X-RAY DIFFRACTION100
2.978-3.40880.18891700.15782766X-RAY DIFFRACTION100
3.4088-4.29390.16681730.13342772X-RAY DIFFRACTION100
4.2939-39.57560.16451500.14212961X-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)
10.4361-0.2281-0.10780.60520.40390.9873-0.00930.0097-0.0208-0.0163-0.02450.0450.0839-0.0478-0.02550.1062-0.00390.00480.0977-0.01830.095639.427637.607714.9669
20.3315-0.2415-0.39610.4752-0.01170.7228-0.0121-0.0269-0.04870.0310.01710.01290.09310.0580.00230.08450.0056-0.00270.0968-0.0070.087829.806745.430637.2464
30.0716-0.01320.1270.07-0.17770.3342-0.01710.08330.03390.0322-0.01-0.0414-0.05980.0021-0.00230.0937-0.00050.0050.1052-0.00060.095425.024156.13632.1545
40.428-0.04440.15290.2861-0.36980.2835-0.0092-0.0003-0.007-0.0476-0.0057-0.0534-0.03650.0198-00.09760.0012-0.00250.104-0.02080.114433.084663.249420.9449
50.0431-0.1072-0.0595-0.0075-0.20910.1595-0.00550.0131-0.0639-0.01950.0109-0.0285-0.03020.0289-0.010.09610.00250.00740.0811-0.01290.100123.769859.883729.0703
60.47650.27330.12410.4040.05880.4875-0.01130.0797-0.0708-0.03910.0153-0.0126-0.0055-0.02130.00310.11210.00070.00050.0999-0.02050.11314.097263.6910.1129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 228 )
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 269 )
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 330 )
5X-RAY DIFFRACTION5chain 'A' and (resid 331 through 377 )
6X-RAY DIFFRACTION6chain 'A' and (resid 378 through 448 )

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