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- PDB-6nn1: Xanthomonas citri PGM Apo-Dephospho -

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Basic information

Entry
Database: PDB / ID: 6nn1
TitleXanthomonas citri PGM Apo-Dephospho
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _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)51,5756
Polymers51,1371
Non-polymers4385
Water9,206511
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)44.020, 54.610, 171.960
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: 51137.496 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 39.14 %
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: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.5→44.02 Å / Num. obs: 67541 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.03 / Rrim(I) all: 0.111 / Net I/σ(I): 14.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 12 % / Rmerge(I) obs: 2.95 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3302 / CC1/2: 0.36 / Rpim(I) all: 0.884 / Rrim(I) all: 3.081 / % 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: 1.5→44.02 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.62
RfactorNum. reflection% reflection
Rfree0.2054 3277 4.86 %
Rwork0.1722 --
obs0.1739 67460 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 27 511 3984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063703
X-RAY DIFFRACTIONf_angle_d0.845033
X-RAY DIFFRACTIONf_dihedral_angle_d4.4422983
X-RAY DIFFRACTIONf_chiral_restr0.054545
X-RAY DIFFRACTIONf_plane_restr0.006675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52240.37691490.35422768X-RAY DIFFRACTION100
1.5224-1.54620.36481380.31662707X-RAY DIFFRACTION100
1.5462-1.57150.32781480.30032786X-RAY DIFFRACTION100
1.5715-1.59860.30011330.26892727X-RAY DIFFRACTION100
1.5986-1.62770.29781190.25352780X-RAY DIFFRACTION100
1.6277-1.6590.27351260.25632765X-RAY DIFFRACTION100
1.659-1.69290.29691380.24472755X-RAY DIFFRACTION100
1.6929-1.72970.25171440.2282733X-RAY DIFFRACTION100
1.7297-1.76990.24491510.21062779X-RAY DIFFRACTION100
1.7699-1.81420.23711420.19152743X-RAY DIFFRACTION100
1.8142-1.86330.22441410.19082774X-RAY DIFFRACTION100
1.8633-1.91810.22621400.192770X-RAY DIFFRACTION100
1.9181-1.980.25041240.18382786X-RAY DIFFRACTION100
1.98-2.05080.21071510.18952757X-RAY DIFFRACTION100
2.0508-2.13290.21471370.17652798X-RAY DIFFRACTION100
2.1329-2.230.1871390.1622790X-RAY DIFFRACTION100
2.23-2.34750.19011340.16762806X-RAY DIFFRACTION100
2.3475-2.49460.20261420.16622802X-RAY DIFFRACTION100
2.4946-2.68730.19611650.16582785X-RAY DIFFRACTION100
2.6873-2.95770.22661520.17122830X-RAY DIFFRACTION100
2.9577-3.38570.19821540.16042842X-RAY DIFFRACTION100
3.3857-4.26560.1861480.13232866X-RAY DIFFRACTION100
4.2656-86.12160.14291620.13883034X-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)
10.3038-0.4199-0.00140.50280.1390.43510.0340.0532-0.068-0.0888-0.06680.10910.11730.0299-00.21370.01150.02220.1787-0.04370.179936.844435.79912.8363
20.0976-0.1102-0.16560.68910.02090.5569-0.0206-0.03780.00440.02040.06050.04070.09190.023-00.15730.02530.02480.1722-0.02990.164141.616539.480520.2831
30.3175-0.225-0.34210.48350.4660.8664-0.0094-0.0794-0.0086-0.01440.0373-0.02070.05920.1651-00.15960.01690.00680.1871-0.01550.162738.766943.872328.9285
4-0.0060.0291-0.09920.3299-0.210.5573-0.01730.02160.0004-0.007-0.003-0.02720.0003-0.034600.1368-0.00130.02260.1585-0.00980.169328.176856.114427.9537
50.1073-0.0370.06810.3527-0.36650.2004-0.0010.0048-0.0902-0.01710.0830.0027-0.03840.0624-00.20610.01080.01780.1673-0.02090.166916.990461.991325.2921
60.08860.03160.00250.2531-0.18320.2734-0.01360.12250.0092-0.19990.0917-0.1001-0.09110.05140.00010.2510.01490.00880.2188-0.01520.20215.896367.21725.587
70.24290.2336-0.03240.3376-0.32390.37630.02410.0919-0.03950.00350.03080.040.0354-0.062500.18190.00540.01180.166-0.03040.189613.084461.351312.8161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:71 )A23 - 71
2X-RAY DIFFRACTION2( CHAIN A AND RESID 72:135 )A72 - 135
3X-RAY DIFFRACTION3( CHAIN A AND RESID 136:219 )A136 - 219
4X-RAY DIFFRACTION4( CHAIN A AND RESID 220:372 )A220 - 372
5X-RAY DIFFRACTION5( CHAIN A AND RESID 373:399 )A373 - 399
6X-RAY DIFFRACTION6( CHAIN A AND RESID 400:430 )A400 - 430
7X-RAY DIFFRACTION7( CHAIN A AND RESID 431:448 )A431 - 448

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