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- PDB-6nqh: Xanthomonas citri Dephospho-PGM in complex with xylose-1-phosphate -

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Basic information

Entry
Database: PDB / ID: 6nqh
TitleXanthomonas citri Dephospho-PGM in complex with xylose-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, 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-xylopyranose / 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: To Be Published
Title: Substate dynamics of the XcPGM reaction mechanism
Authors: Stiers, K.M. / Beamer, L.J.
History
DepositionJan 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / 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 1.2Oct 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)51,8364
Polymers51,3521
Non-polymers4853
Water7,368409
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)43.863, 54.626, 173.359
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: Sugar ChemComp-X1P / 1-O-phosphono-alpha-D-xylopyranose / 1-O-phosphono-alpha-D-xylose / 1-O-phosphono-D-xylose / 1-O-phosphono-xylose


Type: D-saccharide / Mass: 230.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 39.18 %
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: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.45→57.79 Å / Num. obs: 54627 / % possible obs: 72.8 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 18.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2590 / CC1/2: 0.564 / Rpim(I) all: 0.398 / Rrim(I) all: 0.762 / % possible all: 70.5

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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: 1.45→39.697 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 21.32
RfactorNum. reflection% reflection
Rfree0.2147 5281 5.21 %
Rwork0.1773 --
obs0.1792 101364 71.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→39.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 29 409 3870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063559
X-RAY DIFFRACTIONf_angle_d0.8564839
X-RAY DIFFRACTIONf_dihedral_angle_d4.4442077
X-RAY DIFFRACTIONf_chiral_restr0.077537
X-RAY DIFFRACTIONf_plane_restr0.006639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.33911770.28862868X-RAY DIFFRACTION63
1.4665-1.48370.38221650.31443009X-RAY DIFFRACTION67
1.4837-1.50180.31781560.28313249X-RAY DIFFRACTION72
1.5018-1.52080.31341880.27863493X-RAY DIFFRACTION76
1.5208-1.54090.26492060.25553619X-RAY DIFFRACTION81
1.5409-1.5620.25162380.22323941X-RAY DIFFRACTION87
1.562-1.58430.25392400.21684052X-RAY DIFFRACTION91
1.5843-1.60790.26062480.20924271X-RAY DIFFRACTION95
1.6079-1.63310.24922660.20314399X-RAY DIFFRACTION98
1.6331-1.65980.26662270.19814548X-RAY DIFFRACTION100
1.6598-1.68850.26452320.19324518X-RAY DIFFRACTION100
1.6885-1.71920.2127200.2205206X-RAY DIFFRACTION42
1.7192-1.75220.482580.2339115X-RAY DIFFRACTION24
1.7522-1.7880.23992440.18274347X-RAY DIFFRACTION99
1.788-1.82690.24832300.17754517X-RAY DIFFRACTION99
1.8269-1.86940.22951200.17962599X-RAY DIFFRACTION91
1.9679-2.02580.20531980.18913348X-RAY DIFFRACTION88
2.0258-2.09120.1886450.1909983X-RAY DIFFRACTION87
2.0912-2.16590.19112260.16743684X-RAY DIFFRACTION94
2.1659-2.25270.24941710.16722723X-RAY DIFFRACTION96
2.2527-2.35520.19071550.1713203X-RAY DIFFRACTION96
2.3552-2.47930.19042390.17234512X-RAY DIFFRACTION100
2.4793-2.63460.19212760.17174448X-RAY DIFFRACTION100
2.6346-2.8380.22291630.1792885X-RAY DIFFRACTION64
2.838-3.12350.22692010.17854560X-RAY DIFFRACTION100
3.1235-3.57520.21722020.16693888X-RAY DIFFRACTION86
3.5752-4.50340.16411780.13743625X-RAY DIFFRACTION80
4.5034-39.71150.15972620.13784473X-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)
10.9821-0.205-0.15511.77050.5751.9978-0.02460.0782-0.091-0.05830.01990.0460.190.00630.00880.10550.00680.00870.09-0.02690.094839.840637.566815.1453
20.2967-0.0542-0.07380.5233-0.14920.66950.00360.0164-0.0047-0.00010.0083-0.00910.01210.0097-0.01310.0551-00.00330.0815-0.01910.076730.225354.048231.26
31.04980.13691.17030.262-0.41912.3006-0.01220.0385-0.0540.02710.0623-0.03510.0859-0.0128-0.04820.06640.00160.02490.0567-0.0060.070217.018961.93925.2863
42.3598-0.4351-0.52152.09520.84012.5364-0.04010.1645-0.1159-0.17520.0894-0.07550.07690.0527-0.04050.0959-0.0088-0.00410.0816-0.01110.079414.339263.715310.215
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 165:372 )A165 - 372
3X-RAY DIFFRACTION3( CHAIN A AND RESID 373:399 )A373 - 399
4X-RAY DIFFRACTION4( CHAIN A AND RESID 400:448 )A400 - 448

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