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- PDB-4qg5: Crystal structure of phosphoglucomutase from Leishmania major at ... -

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Basic information

Entry
Database: PDB / ID: 4qg5
TitleCrystal structure of phosphoglucomutase from Leishmania major at 3.5 angstrom resolution
ComponentsPutative phosphoglucomutase
KeywordsISOMERASE / Phosphohexomutase / Phosphotransferase / metal-binding region / Alpha and beta proteins
Function / homology
Function and homology information


intramolecular phosphotransferase activity / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytosol
Similarity search - Function
Phosphoglucomutase / 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 / 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
phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsWaugh, B. / Sen, U. / Banerjee, R.
CitationJournal: To be Published
Title: Crystal structure of phosphoglucomutase from Leishmania major at 3.5 angstrom resolution
Authors: Waugh, B. / Sen, U. / Banerjee, R.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Experimental preparation
Revision 1.2Nov 8, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phosphoglucomutase
B: Putative phosphoglucomutase
C: Putative phosphoglucomutase
D: Putative phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,0828
Polymers256,9844
Non-polymers974
Water00
1
A: Putative phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2702
Polymers64,2461
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2702
Polymers64,2461
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2702
Polymers64,2461
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2702
Polymers64,2461
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)202.358, 114.971, 125.915
Angle α, β, γ (deg.)90.00, 110.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative phosphoglucomutase


Mass: 64246.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LMJF_21_0640 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q4QCF1, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293 K / pH: 8
Details: 0.1M Tris-HCl, pH 8.0, 10% (w/v) PEG 3350, 10mM MgCl2, 0.02% Sodium Azide, Hanging drop vapor diffusion method, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 3.5→39.655 Å / Num. obs: 29659 / % possible obs: 86.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 8.3
Reflection shellResolution: 3.5→3.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.3 / % possible all: 88.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PMG

3pmg


Resolution: 3.5→38.167 Å / SU ML: 0.62 / σ(F): 1.34 / Phase error: 35.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3147 1488 5.02 %
Rwork0.2379 --
obs0.2417 29635 86.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→38.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17132 0 4 0 17136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717546
X-RAY DIFFRACTIONf_angle_d1.01923858
X-RAY DIFFRACTIONf_dihedral_angle_d15.6386229
X-RAY DIFFRACTIONf_chiral_restr0.0352688
X-RAY DIFFRACTIONf_plane_restr0.0063128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.6130.40911140.30082633X-RAY DIFFRACTION89
3.613-3.7420.37821400.29092607X-RAY DIFFRACTION88
3.742-3.89170.35371540.28062576X-RAY DIFFRACTION88
3.8917-4.06860.36041270.26192564X-RAY DIFFRACTION87
4.0686-4.28280.30351310.23882594X-RAY DIFFRACTION88
4.2828-4.55080.2991470.21822545X-RAY DIFFRACTION87
4.5508-4.90150.30351410.2132555X-RAY DIFFRACTION86
4.9015-5.39350.29771350.22182548X-RAY DIFFRACTION86
5.3935-6.17110.36541270.26152537X-RAY DIFFRACTION85
6.1711-7.76420.27781490.25072514X-RAY DIFFRACTION84
7.7642-38.16910.25041230.18342474X-RAY DIFFRACTION81

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