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- PDB-4gde: Crystal structure of NADPH-reduced Aspergillus fumigatus UDP-gala... -

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Basic information

Entry
Database: PDB / ID: 4gde
TitleCrystal structure of NADPH-reduced Aspergillus fumigatus 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTanner, J.J. / Dhatwalia, R.D. / Singh, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Identification of the NAD(P)H Binding Site of Eukaryotic UDP-Galactopyranose Mutase.
Authors: Dhatwalia, R. / Singh, H. / Solano, L.M. / Oppenheimer, M. / Robinson, R.M. / Ellerbrock, J.F. / Sobrado, P. / Tanner, J.J.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Sep 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
C: UDP-galactopyranose mutase
D: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,91321
Polymers228,5144
Non-polymers4,39917
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-55 kcal/mol
Surface area75840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.451, 217.451, 319.867
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: 57128.484 Da / Num. of mol.: 4 / Mutation: K344A, K345A, A429T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: GLF / 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.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT A429T IS AN UNINTENDED MUTATION ON THE SURFACE OF THE PROTEIN.

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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: 4.78 Å3/Da / Density % sol: 74.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.4M ammonium sulfate, 0.1M sodium acetate, pH 4.5., vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→49.65 Å / Num. all: 222394 / Num. obs: 222394 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rsym value: 0.093 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.3240.6731.2127933322330.67399.8
2.32-2.464.30.4741.6131430305160.474100
2.46-2.634.50.3342.3130120287680.334100
2.63-2.844.60.2213.5123950268050.22199.9
2.84-3.114.60.1455.2114688246810.14599.8
3.11-3.484.60.0957.5102742223860.09599.7
3.48-4.024.50.06710.288638197750.06799.5
4.02-4.924.40.05212.373939167450.05299.1
4.92-6.964.40.04414.458218130850.04498.8
6.96-49.654.40.03213.13251174000.03297.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTF

3utf


Resolution: 2.2→48.431 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8541 / SU ML: 0.36 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 11121 5 %Same test set that was used in refinement of 3UTE, 3UTF, 3UTG, and 3UTH.
Rwork0.2008 ---
obs0.2021 222338 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.843 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 169.29 Å2 / Biso mean: 40.5832 Å2 / Biso min: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.9304 Å20 Å20 Å2
2---2.9304 Å2-0 Å2
3---5.8608 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15518 0 277 435 16230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716203
X-RAY DIFFRACTIONf_angle_d1.05422142
X-RAY DIFFRACTIONf_chiral_restr0.0672429
X-RAY DIFFRACTIONf_plane_restr0.0052859
X-RAY DIFFRACTIONf_dihedral_angle_d14.8245898
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 (%)
2.2-2.27860.343110870.29312092422011100
2.2786-2.36990.286610840.2552098822072100
2.3699-2.47770.294911240.24742099122115100
2.4777-2.60830.274611170.2322098822105100
2.6083-2.77170.264810920.21852107322165100
2.7717-2.98570.26610780.21972112422202100
2.9857-3.28610.247311340.22372110222236100
3.2861-3.76150.24711360.2162211562229299
3.7615-4.73840.165210970.1507212262232399
4.7384-48.44270.176911720.1671216452281798
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)
10.99770.0263-0.26580.2155-0.01310.33960.02430.2937-0.07350.0071-0.0053-0.0651-0.0078-0.0268-0.01460.08180.03770.03140.2462-0.02820.153271.612177.648159.5685
20.5174-0.40380.05450.6496-0.0050.2561-0.1674-0.06730.01170.18820.1160.0958-0.0436-0.01830.04060.21350.07730.03230.1625-0.0160.206824.5095102.8645211.769
31.01640.18980.08720.1620.05310.2425-0.0130.4296-0.1736-0.01170.07450.04050.03790.0411-0.05960.14760.0322-0.05840.389-0.10380.215625.845268.0693149.5014
40.3561-0.36520.08070.9257-0.06960.1132-0.1621-0.0776-0.15160.34530.24190.1938-0.0278-0.0499-0.05740.26370.1320.08190.20020.12660.210642.082859.3539221.8592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 506
2X-RAY DIFFRACTION2chain BB3 - 506
3X-RAY DIFFRACTION3chain CC3 - 507
4X-RAY DIFFRACTION4chain DD3 - 506

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