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- PDB-6nqe: Xanthomonas citri PGM Apo-Dephospho at room temperature -

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Basic information

Entry
Database: PDB / ID: 6nqe
TitleXanthomonas citri PGM Apo-Dephospho at room temperature
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
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 21, 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 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)51,3762
Polymers51,3521
Non-polymers241
Water2,846158
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)44.360, 55.620, 174.850
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
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: 298 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: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.85→53.003 Å / Num. obs: 37952 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.051 / Rrim(I) all: 0.134 / Net I/σ(I): 10.1
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.081 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2257 / CC1/2: 0.375 / Rpim(I) all: 0.852 / Rrim(I) all: 2.254 / % possible all: 100

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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: 1.85→53.003 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.64
RfactorNum. reflection% reflection
Rfree0.1873 1907 5.03 %
Rwork0.1607 --
obs0.1621 37880 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→53.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 1 158 3605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063697
X-RAY DIFFRACTIONf_angle_d0.8765041
X-RAY DIFFRACTIONf_dihedral_angle_d6.1852980
X-RAY DIFFRACTIONf_chiral_restr0.054545
X-RAY DIFFRACTIONf_plane_restr0.006686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.33431220.322488X-RAY DIFFRACTION100
1.8963-1.94750.29271540.2642506X-RAY DIFFRACTION100
1.9475-2.00490.2731450.22912527X-RAY DIFFRACTION100
2.0049-2.06960.26031150.21022547X-RAY DIFFRACTION100
2.0696-2.14350.22761570.18832537X-RAY DIFFRACTION100
2.1435-2.22940.18871190.16832566X-RAY DIFFRACTION100
2.2294-2.33080.16891340.16742539X-RAY DIFFRACTION100
2.3308-2.45370.23681250.16692563X-RAY DIFFRACTION100
2.4537-2.60740.19211460.17442539X-RAY DIFFRACTION100
2.6074-2.80880.22781320.17482566X-RAY DIFFRACTION100
2.8088-3.09140.2351270.1782610X-RAY DIFFRACTION100
3.0914-3.53860.18611300.15352593X-RAY DIFFRACTION100
3.5386-4.4580.14061410.11492642X-RAY DIFFRACTION100
4.458-53.02470.13791600.13472750X-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)
10.6763-0.623-0.28841.34370.80171.2440.00960.124-0.0106-0.0532-0.07570.03520.24750.17-0.05370.21850.03710.0350.2299-0.02770.186440.926938.337817.895
20.6589-0.2379-0.11240.8233-0.18431.1491-0.05210.03360.04630.01620.027-0.0369-0.00790.0096-00.1207-0.00570.01930.1347-0.00660.156829.039154.830831.3849
30.30040.13-0.1070.0727-0.10540.11620.0325-0.0321-0.0080.01050.0380.10550.0406-0.2820.00020.28980.06040.02010.2406-0.01660.212416.614262.228426.1436
40.4670.13220.27350.8393-0.30740.49570.04820.30290.0405-0.14060.01330.1384-0.1294-0.0848-00.240.0363-0.00870.2744-0.01170.220514.154164.299810.4359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:181 )A23 - 181
2X-RAY DIFFRACTION2( CHAIN A AND RESID 182:372 )A182 - 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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