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- PDB-4wx1: Structure of Aspergillus fumigatus UDP-Galactopyranose mutase mut... -

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Basic information

Entry
Database: PDB / ID: 4wx1
TitleStructure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant F66A determined from a crystal soaked with UDP-Galactopyranose
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / FLAVIN ADENINE DINUCLEOTIDE BINDING / NUCLEOTIDE BINDING / MUTASE
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 speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsQureshi, I.A. / Chaudhary, R.
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
DepositionNov 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / 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_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)233,21721
Polymers228,2104
Non-polymers5,00717
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17460 Å2
ΔGint-182 kcal/mol
Surface area72330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.943, 217.943, 321.122
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
UDP-galactopyranose mutase


Mass: 57052.391 Da / Num. of mol.: 4 / Mutation: F66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: glf, glfA / Production host: Escherichia coli (E. coli) / References: UniProt: Q4W1X2, UDP-galactopyranose mutase

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Non-polymers , 5 types, 553 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.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 4.82 Å3/Da / Density % sol: 74.5 %
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. Crystal was soaked in 100 mM UDP-galactopyranose for 75 minutes.
PH range: 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: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→162.72 Å / Num. obs: 224393 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 32.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.048 / Net I/σ(I): 13.1 / Num. measured all: 2997337 / Scaling rejects: 404
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
2.2-2.2413.81.4032151455109990.5650.392100
12.05-162.7212.20.02740.418896154610.00897.7

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3UTG

3utg


Resolution: 2.2→103.192 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 11257 5.02 %
Rwork0.1878 213108 -
obs0.1895 224365 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.49 Å2 / Biso mean: 40.2672 Å2 / Biso min: 19.01 Å2
Refinement stepCycle: final / Resolution: 2.2→103.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15479 0 319 536 16334
Biso mean--39.23 37.37 -
Num. residues----2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716195
X-RAY DIFFRACTIONf_angle_d1.0722144
X-RAY DIFFRACTIONf_chiral_restr0.0392442
X-RAY DIFFRACTIONf_plane_restr0.0052855
X-RAY DIFFRACTIONf_dihedral_angle_d15.4345932
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 (%)
2.2-2.2250.33733990.289469907389100
2.225-2.25120.32143500.286870647414100
2.2512-2.27860.29353780.269970247402100
2.2786-2.30750.30453660.267570877453100
2.3075-2.33780.3163690.259970617430100
2.3378-2.36990.27093680.254370487416100
2.3699-2.40370.27693670.242570547421100
2.4037-2.43960.28323610.242270707431100
2.4396-2.47770.284010.236570497450100
2.4777-2.51840.25613590.232370767435100
2.5184-2.56180.27743770.232270277404100
2.5618-2.60840.26214040.225970627466100
2.6084-2.65860.2723540.223370977451100
2.6586-2.71280.26393660.219370647430100
2.7128-2.77180.26113750.220370797454100
2.7718-2.83630.25943400.213471147454100
2.8363-2.90720.26163600.21870987458100
2.9072-2.98580.28223780.215871007478100
2.9858-3.07370.24254080.20970337441100
3.0737-3.17290.23733570.213771047461100
3.1729-3.28630.23073820.199370937475100
3.2863-3.41790.25424080.201170817489100
3.4179-3.57350.18743660.18257113747999
3.5735-3.76190.20473670.1687132749999
3.7619-3.99760.18283480.15067161750999
3.9976-4.30630.16174000.13497116751699
4.3063-4.73960.14433580.12377203756199
4.7396-5.42540.163950.13047161755699
5.4254-6.83530.20123870.16097252763998
6.8353-103.30540.17134090.15467495790497
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)
11.3603-0.1299-0.26310.22340.07350.6302-0.040.3053-0.0204-0.0163-0.0048-0.0399-0.0146-0.05830.03390.20640.0220.04350.3584-0.00940.427571.692277.7795160.4279
20.5885-0.3355-0.010.5696-0.05970.6711-0.0891-0.05620.0070.15380.03860.068-0.0298-0.01850.0450.27950.04460.01960.2101-0.03190.362924.6005103.4095212.5957
31.1986-0.0021-0.10550.33370.08780.8954-0.02460.4334-0.2393-0.07350.0631-0.03660.1160.0878-0.03290.21650.0082-0.0370.4333-0.10780.386825.762668.2562150.5228
40.7102-0.5791-0.11120.98660.15750.7144-0.1193-0.1132-0.14820.32740.13790.18930.0412-0.0472-0.0180.32830.06070.04120.24130.0840.386442.295259.9338222.916
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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