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- PDB-6nn2: Xanthomonas citri PGM Apo-Phospho -

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Basic information

Entry
Database: PDB / ID: 6nn2
TitleXanthomonas citri PGM Apo-Phospho
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 superfamily / Alpha-D-phosphohexomutase, C-terminal domain / 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 superfamily / Alpha-D-phosphohexomutase, C-terminal domain / 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
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 14, 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)51,7543
Polymers51,4321
Non-polymers3222
Water11,854658
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)43.789, 54.734, 174.255
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: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
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: 1.44→46.35 Å / Num. obs: 76942 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 14.2
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 4 % / Rmerge(I) obs: 1.358 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3750 / CC1/2: 0.313 / Rpim(I) all: 0.755 / Rrim(I) all: 1.564 / % possible all: 99.3

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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: 1.44→46.35 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 19.87
RfactorNum. reflection% reflection
Rfree0.2076 3713 4.83 %
Rwork0.1708 --
obs0.1725 76879 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.44→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 20 658 4128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053768
X-RAY DIFFRACTIONf_angle_d0.8745130
X-RAY DIFFRACTIONf_dihedral_angle_d6.8922148
X-RAY DIFFRACTIONf_chiral_restr0.083552
X-RAY DIFFRACTIONf_plane_restr0.006693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.45820.35671420.35332675X-RAY DIFFRACTION100
1.4582-1.47740.32881250.312654X-RAY DIFFRACTION100
1.4774-1.49770.30411330.28572689X-RAY DIFFRACTION100
1.4977-1.51910.28481270.27072680X-RAY DIFFRACTION100
1.5191-1.54170.29591400.25632635X-RAY DIFFRACTION100
1.5417-1.56580.26621450.22632743X-RAY DIFFRACTION100
1.5658-1.59150.24851490.2152611X-RAY DIFFRACTION100
1.5915-1.61890.20841290.2072719X-RAY DIFFRACTION100
1.6189-1.64840.23821190.2052642X-RAY DIFFRACTION100
1.6484-1.68010.25781370.19952707X-RAY DIFFRACTION100
1.6801-1.71440.21061290.20012695X-RAY DIFFRACTION100
1.7144-1.75170.24871350.19982711X-RAY DIFFRACTION100
1.7517-1.79240.21541180.20962671X-RAY DIFFRACTION100
1.7924-1.83720.21791480.19652688X-RAY DIFFRACTION100
1.8372-1.88690.25391520.18272681X-RAY DIFFRACTION100
1.8869-1.94240.20261350.17332682X-RAY DIFFRACTION100
1.9424-2.00510.21691520.1732702X-RAY DIFFRACTION100
2.0051-2.07680.20071630.16562673X-RAY DIFFRACTION100
2.0768-2.160.19941270.16082696X-RAY DIFFRACTION100
2.16-2.25830.21841530.16022725X-RAY DIFFRACTION100
2.2583-2.37730.17591410.15982698X-RAY DIFFRACTION100
2.3773-2.52630.16791520.1532716X-RAY DIFFRACTION100
2.5263-2.72130.19321370.15442753X-RAY DIFFRACTION100
2.7213-2.99520.20291430.1582731X-RAY DIFFRACTION100
2.9952-3.42850.18111320.14982796X-RAY DIFFRACTION100
3.4285-4.31920.1841220.12872821X-RAY DIFFRACTION100
4.3192-52.2530.17721280.14462972X-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)
10.3117-0.0967-0.16190.680.60410.9967-0.0410.0013-0.0517-0.0116-0.02220.06210.13710.0312-0.00550.10270.01310.01070.086-0.02210.097740.222838.096317.2008
20.2123-0.0851-0.09290.4052-0.20080.6248-0.00920.00430.0013-0.00130.0041-0.0198-0.02640.009-0.00050.0961-0.00290.00110.1217-0.01540.117428.082555.676831.6674
30.7459-0.0104-0.00280.54180.1080.98870.02450.1154-0.0518-0.09440.0209-0.0030.03360.00780.00220.11910.0074-0.00670.0973-0.01680.10913.88362.370210.6153
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 182:386 )A182 - 386
3X-RAY DIFFRACTION3( CHAIN A AND RESID 387:448 )A387 - 448

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