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- PDB-4dsg: Crystal Structure of oxidized UDP-Galactopyranose mutase -

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Basic information

Entry
Database: PDB / ID: 4dsg
TitleCrystal Structure of oxidized UDP-Galactopyranose mutase
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / Rossmann fold / flavin adenine dinucleotide
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
NAD(P)-binding Rossmann-like domain / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / Amine oxidase domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.249 Å
AuthorsSingh, H. / Dhatwalia, R. / Tanner, J.J.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal Structures of Trypanosoma cruzi UDP-Galactopyranose Mutase Implicate Flexibility of the Histidine Loop in Enzyme Activation.
Authors: Dhatwalia, R. / Singh, H. / Oppenheimer, M. / Sobrado, P. / Tanner, J.J.
History
DepositionFeb 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 13, 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 / 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 / _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: UDP-galactopyranose mutase
B: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9327
Polymers110,4572
Non-polymers2,4755
Water6,864381
1
A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5144
Polymers55,2281
Non-polymers1,2863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4183
Polymers55,2281
Non-polymers1,1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.393, 143.393, 354.205
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein UDP-galactopyranose mutase /


Mass: 55228.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053507993.160 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4E1W2, UDP-galactopyranose mutase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 4.76 Å3/Da / Density % sol: 74.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.0 M ammonium sulfate, 0.5% PEG8000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2011 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.249→55 Å / Num. all: 102574 / Num. obs: 101725 / % possible obs: 99.2 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.105 / Χ2: 0.791 / Net I/σ(I): 14.077
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.249-2.335.20.5422.214193810.559100
2.33-2.426.40.552193700.553100
2.42-2.536.40.44193330.55599.9
2.53-2.676.40.339193810.57599.9
2.67-2.836.40.237193170.60899.8
2.83-3.056.40.161193890.6799.8
3.05-3.366.40.111192830.77199.7
3.36-3.856.40.085193131.1999.5
3.85-4.856.40.068193161.59199.3
4.85-556.40.041192360.84598.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UTE

3ute


Resolution: 2.249→46.936 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8723 / SU ML: 0.32 / σ(F): 0 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 5093 5.01 %RANDOM
Rwork0.1829 ---
obs0.1844 101705 99.21 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.646 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 109.33 Å2 / Biso mean: 29.9405 Å2 / Biso min: 5.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.8856 Å20 Å2-0 Å2
2--2.8856 Å20 Å2
3----5.7712 Å2
Refinement stepCycle: LAST / Resolution: 2.249→46.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7479 0 161 381 8021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077901
X-RAY DIFFRACTIONf_angle_d1.12210801
X-RAY DIFFRACTIONf_chiral_restr0.0751138
X-RAY DIFFRACTIONf_plane_restr0.0051372
X-RAY DIFFRACTIONf_dihedral_angle_d15.182927
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.249-2.32970.29795080.2463950610014100
2.3297-2.4230.27414860.2221959410080100
2.423-2.53320.25244810.2085959810079100
2.5332-2.66680.25125310.2045959510126100
2.6668-2.83380.22815010.1941959510096100
2.8338-3.05260.23365150.1928965210167100
3.0526-3.35970.24554990.194296671016699
3.3597-3.84570.20555040.184596911019599
3.8457-4.84440.1475240.134197641028899
4.8444-46.94660.18785440.172599501049496
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)
10.08250.037-0.04591.3368-0.69570.3578-0.0031-0.014-0.01010.2667-0.05240.0702-0.1457-0.00980.03040.1345-0.04240.0034-0.00730.01280.033865.9513-12.1473-35.0285
20.4318-0.0193-0.21590.2690.19970.44810.0023-0.12160.0948-0.02730.05650.0174-0.01880.1783-0.05870.0141-0.0285-0.02630.1104-0.02430.064569.772-41.2222-67.8647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA4 - 476
2X-RAY DIFFRACTION2chain BB6 - 476

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