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- PDB-4u8p: Structure of Aspergillus fumigatus UDP-Galactopyranose mutase mut... -

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Basic information

Entry
Database: PDB / ID: 4u8p
TitleStructure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant Y317A complexed with UDP
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / NUCLEOTIDE BINDING / MUTASE / FLAVIN ADENINE DINUCLEOTIDE BINDING
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / cell wall organization / 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 / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 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)237,59261
Polymers228,1464
Non-polymers9,44657
Water21,9421218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25420 Å2
ΔGint-189 kcal/mol
Surface area73720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.248, 217.248, 320.856
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
UDP-galactopyranose mutase


Mass: 57036.391 Da / Num. of mol.: 4 / Mutation: Y317A, 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

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Non-polymers , 5 types, 1275 molecules

#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1218 / 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: 4.79 Å3/Da / Density % sol: 74.32 %
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: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CMOS / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→61.04 Å / Num. obs: 275353 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.043 / Net I/σ(I): 14.4 / Num. measured all: 2047696 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.05-2.097.31.0452.498709134520.7750.40399.9
11.23-61.046.70.02442.61242318640.9990.0197.2

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Processing

Software
NameVersionClassification
XDS0.2.17data reduction
Cootmodel building
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UTF

3utf


Resolution: 2.05→55.25 Å / FOM work R set: 0.879 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 13798 5.01 %
Rwork0.1676 261357 -
obs0.1689 275155 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.47 Å2 / Biso mean: 30.77 Å2 / Biso min: 13.61 Å2
Refinement stepCycle: final / Resolution: 2.05→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15524 0 563 1218 17305
Biso mean--42.93 35.1 -
Num. residues----2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716456
X-RAY DIFFRACTIONf_angle_d1.0322451
X-RAY DIFFRACTIONf_chiral_restr0.0392463
X-RAY DIFFRACTIONf_plane_restr0.0062867
X-RAY DIFFRACTIONf_dihedral_angle_d15.2486113
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 (%)
2.05-2.07330.28934620.247685318993100
2.0733-2.09770.25954460.225386669112100
2.0977-2.12330.23574490.207986579106100
2.1233-2.15010.23894450.19686729117100
2.1501-2.17840.23754530.199586169069100
2.1784-2.20830.22614850.194185879072100
2.2083-2.23980.2444420.211887029144100
2.2398-2.27330.27574640.226585509014100
2.2733-2.30880.21764530.18787159168100
2.3088-2.34660.22894590.182886039062100
2.3466-2.38710.24344240.18687249148100
2.3871-2.43050.21644600.174486159075100
2.4305-2.47730.21184940.173586669160100
2.4773-2.52780.20854350.172586989133100
2.5278-2.58280.20364940.171286499143100
2.5828-2.64290.21234460.173286589104100
2.6429-2.7090.20374550.171887149169100
2.709-2.78220.21314370.177487069143100
2.7822-2.86410.21244340.174787239157100
2.8641-2.95650.20894480.173586979145100
2.9565-3.06220.19854920.175187019193100
3.0622-3.18480.22174500.195187249174100
3.1848-3.32970.20484690.179487189187100
3.3297-3.50520.20274940.177987299223100
3.5052-3.72480.18714450.160987519196100
3.7248-4.01230.15194320.14358788922099
4.0123-4.41590.13114820.12388079289100
4.4159-5.05450.13694590.120988929351100
5.0545-6.36670.1564790.144989529431100
6.3667-55.27020.16635110.15469146965798

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