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- PDB-4u8j: Structure of Aspergillus fumigatus UDP-Galactopyranose mutase mut... -

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Basic information

Entry
Database: PDB / ID: 4u8j
TitleStructure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant Y104A
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 / 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)234,31244
Polymers228,1464
Non-polymers6,16740
Water15,511861
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-53 kcal/mol
Surface area76920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.419, 218.419, 322.197
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: 57036.391 Da / Num. of mol.: 4 / Mutation: Y104A, 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


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / 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: 4.86 Å3/Da / Density % sol: 74.7 %
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→163.12 Å / Num. obs: 198787 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 24.07 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.065 / Net I/σ(I): 10 / Num. measured all: 2130460
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
2.3-2.3411.20.7593.110915397170.8190.23699.9
12.6-163.129.80.03419.71364313910.9990.01198.5

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Processing

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

3utf


Resolution: 2.3→163 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 9978 5.02 %
Rwork0.1818 188745 -
obs0.1837 198723 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.07 Å2 / Biso mean: 29.1691 Å2 / Biso min: 11.27 Å2
Refinement stepCycle: final / Resolution: 2.3→163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15563 0 379 861 16803
Biso mean--36.61 31.34 -
Num. residues----2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716314
X-RAY DIFFRACTIONf_angle_d1.02322263
X-RAY DIFFRACTIONf_chiral_restr0.0372432
X-RAY DIFFRACTIONf_plane_restr0.0062868
X-RAY DIFFRACTIONf_dihedral_angle_d15.0995940
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 (%)
2.3-2.32610.33173370.244761736510100
2.3261-2.35350.28543380.237162036541100
2.3535-2.38220.31723030.237362616564100
2.3822-2.41240.29083300.225962226552100
2.4124-2.44410.26173110.215362476558100
2.4441-2.47760.27283650.213862136578100
2.4776-2.5130.26123290.205462266555100
2.513-2.55050.25183090.208362246533100
2.5505-2.59040.28013600.213962196579100
2.5904-2.63280.27573220.208162626584100
2.6328-2.67820.25433220.205462476569100
2.6782-2.72690.26333290.204162536582100
2.7269-2.77940.25513290.202862456574100
2.7794-2.83610.24233020.204363076609100
2.8361-2.89780.25563180.202162266544100
2.8978-2.96520.2373170.204463076624100
2.9652-3.03940.23553530.201762676620100
3.0394-3.12160.25733430.209362606603100
3.1216-3.21340.24873170.206462976614100
3.2134-3.31720.22353430.192462736616100
3.3172-3.43570.25073710.20262346605100
3.4357-3.57330.2253290.193263236652100
3.5733-3.73590.223160.178563166632100
3.7359-3.93290.19693230.167563386661100
3.9329-4.17940.15793370.145163206657100
4.1794-4.50210.14723190.12763516670100
4.5021-4.95520.14783480.123963666714100
4.9552-5.67220.16983340.13466404673899
5.6722-7.14640.16953600.15216451681199
7.1464-163.53420.16433640.14776710707498
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)
10.626-0.0421-0.09020.3015-0.02760.47560.00370.2064-0.0155-0.0526-0.0041-0.0557-0.0095-0.0065-0.00370.14940.01930.03370.2492-0.02720.215871.660478.1296160.7226
20.4211-0.14990.03980.3952-0.00870.5887-0.0614-0.06010.01370.12740.02120.0585-0.0080.00270.04380.1910.03530.01680.1577-0.01260.200124.4375103.6865213.3797
30.89080.0153-0.15560.26430.07830.5699-0.01970.2869-0.1887-0.07060.05090.01360.08990.0254-0.02530.17640.0071-0.03190.2991-0.07520.26925.57168.519150.7311
40.4902-0.3128-0.01810.66140.16770.5234-0.0587-0.0971-0.1460.2450.08920.15820.0354-0.0394-0.02620.2650.05190.03450.20360.06720.270642.234160.1217223.7736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not resname FDAA0
2X-RAY DIFFRACTION2chain B and not resname FDAB0
3X-RAY DIFFRACTION3chain C and not resname FDAC0
4X-RAY DIFFRACTION4chain D and not resname FDAD0

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