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- PDB-5bmn: Crystal Structure of APO form of Phosphoglucomutase from Xanthomo... -

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Basic information

Entry
Database: PDB / ID: 5bmn
TitleCrystal Structure of APO form of Phosphoglucomutase from Xanthomonas citri
ComponentsPhosphoglucomutase
KeywordsISOMERASE / Phosphoglucomutase citrus canker
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: 1.27 Å
AuthorsGoto, L.S. / Pereira, H.M. / Novo Mansur, M.T.M. / Brandao-Neto, J.
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Structural and functional characterization of the phosphoglucomutase from Xanthomonas citri subsp. citri.
Authors: Goto, L.S. / Vessoni Alexandrino, A. / Malvessi Pereira, C. / Silva Martins, C. / D'Muniz Pereira, H. / Brandao-Neto, J. / Marques Novo-Mansur, M.T.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 20, 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)51,2422
Polymers51,2171
Non-polymers241
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.980, 55.180, 174.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoglucomutase


Mass: 51217.473 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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3)
References: UniProt: Q8PGN7, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#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.: 581 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.5 % PEG 1000, 12.5 % PEG 3350, 12.5 % MPD, 30 mM MgCl2, 30 mM CaCl2, 100 mM MOPS/HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.27→52.62 Å / Num. obs: 112663 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 20
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
1.27-1.35.80.6431097.8
5.68-52.625.80.0241099.4

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Processing

Software
NameVersionClassification
xia2data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2K2Y

2k2y


Resolution: 1.27→35.096 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 5639 5.01 %Random selection
Rwork0.1649 106918 --
obs0.166 112557 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.1 Å2 / Biso mean: 20.7957 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 1.27→35.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 1 581 4032
Biso mean--15.54 32.41 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073524
X-RAY DIFFRACTIONf_angle_d1.1184783
X-RAY DIFFRACTIONf_chiral_restr0.077525
X-RAY DIFFRACTIONf_plane_restr0.006636
X-RAY DIFFRACTIONf_dihedral_angle_d13.4911290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.28440.2571820.25023484X-RAY DIFFRACTION97
1.2844-1.29950.24551780.2363440X-RAY DIFFRACTION98
1.2995-1.31540.25551770.23553523X-RAY DIFFRACTION99
1.3154-1.3320.23631910.21863475X-RAY DIFFRACTION98
1.332-1.34960.23041950.2153511X-RAY DIFFRACTION100
1.3496-1.36810.22592210.21353472X-RAY DIFFRACTION99
1.3681-1.38760.21361660.20423526X-RAY DIFFRACTION99
1.3876-1.40830.20431960.20323523X-RAY DIFFRACTION100
1.4083-1.43030.21081680.20193506X-RAY DIFFRACTION99
1.4303-1.45380.23352150.19273520X-RAY DIFFRACTION100
1.4538-1.47880.2081950.18153512X-RAY DIFFRACTION100
1.4788-1.50570.18851900.17833568X-RAY DIFFRACTION100
1.5057-1.53470.18251660.17093544X-RAY DIFFRACTION100
1.5347-1.5660.17912210.16673547X-RAY DIFFRACTION100
1.566-1.60010.18061880.16333537X-RAY DIFFRACTION100
1.6001-1.63730.18672070.16123551X-RAY DIFFRACTION100
1.6373-1.67820.19071880.17083557X-RAY DIFFRACTION100
1.6782-1.72360.21860.16793575X-RAY DIFFRACTION100
1.7236-1.77430.19011880.17063545X-RAY DIFFRACTION100
1.7743-1.83160.17151770.16143595X-RAY DIFFRACTION100
1.8316-1.89710.19171790.16473579X-RAY DIFFRACTION100
1.8971-1.9730.18411630.1663607X-RAY DIFFRACTION100
1.973-2.06280.16382030.1583544X-RAY DIFFRACTION100
2.0628-2.17150.17081900.15453607X-RAY DIFFRACTION100
2.1715-2.30760.19051490.1633648X-RAY DIFFRACTION100
2.3076-2.48570.20051820.16543592X-RAY DIFFRACTION100
2.4857-2.73580.19871930.16973650X-RAY DIFFRACTION100
2.7358-3.13140.19911930.16693643X-RAY DIFFRACTION99
3.1314-3.94440.1661910.14753690X-RAY DIFFRACTION99
3.9444-35.10.16992010.14623847X-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)
10.6598-0.4741-0.83660.76340.90982.2646-0.0434-0.0094-0.05250.00930.0476-0.0040.17070.1225-0.00390.12660.01310.00660.1229-0.01180.136539.150640.108122.7457
20.1521-0.1614-0.00450.4959-0.29230.9996-0.03140.0005-0.01630.00520.00010.0106-0.0385-0.0360.03060.1147-0.00180.01340.1292-0.0140.130126.639856.693428.4743
31.47190.09780.09141.2875-0.01141.53880.07190.2169-0.0423-0.1585-0.01520.0502-0.0249-0.0048-0.06550.13890.0182-0.00670.1243-0.01010.133814.063263.985310.4256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 219 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 220 through 399 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 470 )A0

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