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- PDB-4u8l: Structure of Aspergillus fumigatus UDP-Galactopyranose mutase mut... -

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Basic information

Entry
Database: PDB / ID: 4u8l
TitleStructure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant N207A
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / NUCLEOTIDE BINDING / MUTASE / FLAVIN ADENINE DINUCLEOTIDE BINDING
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / nucleotide binding
Similarity search - Function
NAD(P)-binding Rossmann-like domain / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsQureshi, I.A. / Chaudhary, R. / Tanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094469 United States
CitationJournal: Biochemistry / Year: 2014
Title: Contributions of Unique Active Site Residues of Eukaryotic UDP-Galactopyranose Mutases to Substrate Recognition and Active Site Dynamics.
Authors: Da Fonseca, I. / Qureshi, I.A. / Mehra-Chaudhary, R. / Kizjakina, K. / Tanner, J.J. / Sobrado, P.
History
DepositionAug 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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
C: UDP-galactopyranose mutase
D: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,14152
Polymers228,3424
Non-polymers6,79948
Water13,836768
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-53 kcal/mol
Surface area76610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.181, 218.181, 321.904
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: 57085.461 Da / Num. of mol.: 4 / Mutation: N207A, K344A, K345A, A429T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: glf, glfA / Production host: Escherichia coli (E. coli) / References: UniProt: Q4W1X2, UDP-galactopyranose mutase
#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 4.84 Å3/Da / Density % sol: 74.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.2 - 1.4 M ammonium sulfate and 0.1 M sodium acetate at pH 4.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→122.53 Å / Num. obs: 197338 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 33.6 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.083 / Net I/σ(I): 7.6 / Num. measured all: 954588 / Scaling rejects: 39
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.344.91.1671.44749296670.5630.57299.9
12.6-122.534.40.03119.7588713250.9980.01694.7

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Processing

Software
NameVersionClassification
XDS0.1.29data reduction
Aimlessdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UTF

3utf


Resolution: 2.3→103.319 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 9909 5.03 %
Rwork0.1885 187241 -
obs0.1902 197150 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.38 Å2 / Biso mean: 37.378 Å2 / Biso min: 19.57 Å2
Refinement stepCycle: final / Resolution: 2.3→103.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15555 0 415 768 16738
Biso mean--45.57 37.7 -
Num. residues----2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816338
X-RAY DIFFRACTIONf_angle_d1.06122295
X-RAY DIFFRACTIONf_chiral_restr0.0392432
X-RAY DIFFRACTIONf_plane_restr0.0062864
X-RAY DIFFRACTIONf_dihedral_angle_d15.0515928
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.32610.32133380.27661616499100
2.3261-2.35350.32253300.26461876517100
2.3535-2.38220.30443000.260762086508100
2.3822-2.41240.31483270.25361986525100
2.4124-2.44410.29653220.242762206542100
2.4441-2.47760.2773580.237662216579100
2.4776-2.5130.2923220.232961946516100
2.513-2.55050.26673250.234261986523100
2.5505-2.59040.28593510.230261866537100
2.5904-2.63280.28373180.232362426560100
2.6328-2.67820.28363200.232861986518100
2.6782-2.7270.26433250.229162306555100
2.727-2.77940.26463280.236562106538100
2.7794-2.83610.28513030.227162826585100
2.8361-2.89780.26133140.215462126526100
2.8978-2.96520.27363180.222862586576100
2.9652-3.03940.26243530.210862076560100
3.0394-3.12160.26373420.216862636605100
3.1216-3.21340.2583180.222562486566100
3.2134-3.31720.24643350.21496220655599
3.3172-3.43570.24953670.22126185655299
3.4357-3.57330.23493280.20156261658999
3.5733-3.73590.22573160.18036230654699
3.7359-3.93290.17993220.15956250657299
3.9329-4.17930.16233320.14986259659199
4.1793-4.5020.15043170.11986272658999
4.502-4.95510.14373410.11866243658498
4.9551-5.6720.16623300.13666312664298
5.672-7.14590.17593490.15626367671698
7.1459-103.42310.163600.15096519687996

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