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- PDB-5vwt: Crystal structure of oxidized Aspergillus fumigatus UDP-galactopy... -

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Basic information

Entry
Database: PDB / ID: 5vwt
TitleCrystal structure of oxidized Aspergillus fumigatus UDP-galactopyranose mutase complexed with NADPH
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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-NDP / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.75 Å
AuthorsTanner, 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: 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
DepositionMay 22, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 31, 2017ID: 4GDC
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)235,98326
Polymers228,5144
Non-polymers7,46922
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19840 Å2
ΔGint-279 kcal/mol
Surface area73400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.292, 218.292, 319.216
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 19 or (resid 20...
21(chain B and (resid 3 through 5 or (resid 6...
31(chain C and (resid 3 through 6 or (resid 7...
41(chain D and (resid 3 through 6 or (resid 7...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLYGLY(chain A and (resid 3 through 19 or (resid 20...AA3 - 196 - 22
12LEULEULEULEU(chain A and (resid 3 through 19 or (resid 20...AA2023
13HISHISALAALA(chain A and (resid 3 through 19 or (resid 20...AA3 - 5056 - 508
14HISHISALAALA(chain A and (resid 3 through 19 or (resid 20...AA3 - 5056 - 508
15HISHISALAALA(chain A and (resid 3 through 19 or (resid 20...AA3 - 5056 - 508
16HISHISALAALA(chain A and (resid 3 through 19 or (resid 20...AA3 - 5056 - 508
17HISHISALAALA(chain A and (resid 3 through 19 or (resid 20...AA3 - 5056 - 508
21HISHISASPASP(chain B and (resid 3 through 5 or (resid 6...BB3 - 56 - 8
22ILEILESERSER(chain B and (resid 3 through 5 or (resid 6...BB6 - 79 - 10
23HISHISALAALA(chain B and (resid 3 through 5 or (resid 6...BB3 - 5056 - 508
24HISHISALAALA(chain B and (resid 3 through 5 or (resid 6...BB3 - 5056 - 508
25HISHISALAALA(chain B and (resid 3 through 5 or (resid 6...BB3 - 5056 - 508
26HISHISALAALA(chain B and (resid 3 through 5 or (resid 6...BB3 - 5056 - 508
31HISHISILEILE(chain C and (resid 3 through 6 or (resid 7...CC3 - 66 - 9
32SERSERSERSER(chain C and (resid 3 through 6 or (resid 7...CC710
33HISHISLYSLYS(chain C and (resid 3 through 6 or (resid 7...CC3 - 5066 - 509
34HISHISLYSLYS(chain C and (resid 3 through 6 or (resid 7...CC3 - 5066 - 509
35HISHISLYSLYS(chain C and (resid 3 through 6 or (resid 7...CC3 - 5066 - 509
36HISHISLYSLYS(chain C and (resid 3 through 6 or (resid 7...CC3 - 5066 - 509
41HISHISILEILE(chain D and (resid 3 through 6 or (resid 7...DD3 - 66 - 9
42SERSERSERSER(chain D and (resid 3 through 6 or (resid 7...DD710
43HISHISLYSLYS(chain D and (resid 3 through 6 or (resid 7...DD3 - 5066 - 509
44HISHISLYSLYS(chain D and (resid 3 through 6 or (resid 7...DD3 - 5066 - 509
45HISHISLYSLYS(chain D and (resid 3 through 6 or (resid 7...DD3 - 5066 - 509
46HISHISLYSLYS(chain D and (resid 3 through 6 or (resid 7...DD3 - 5066 - 509

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Components

#1: Protein
UDP-galactopyranose mutase


Mass: 57128.484 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.8 Å3/Da / Density % sol: 74.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.4 M ammonium sulfate, 0.1 M sodium acetate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2012
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→162.662 Å / Num. all: 116001 / Num. obs: 116001 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 46.92 Å2 / Rpim(I) all: 0.054 / Rrim(I) all: 0.147 / Rsym value: 0.137 / Net I/av σ(I): 5.4 / Net I/σ(I): 11.6 / Num. measured all: 851567
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.75-2.96.10.8850.90.3820.9670.88599.9
2.9-3.076.40.5581.40.2350.6070.55899.9
3.07-3.296.80.3582.20.1470.3880.35899.9
3.29-3.557.10.2423.20.0970.2610.24299.9
3.55-3.897.50.1544.90.0610.1660.15499.9
3.89-4.357.80.1126.50.0430.120.11299.8
4.35-5.028.10.0897.90.0330.0950.08999.9
5.02-6.158.70.0818.70.0290.0860.08199.9
6.15-8.79.30.05811.80.020.0610.05899.9
8.7-162.6628.70.03517.10.0120.0370.03599.5

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3UTF

3utf


Resolution: 2.75→162.662 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.4
RfactorNum. reflection% reflection
Rfree0.2392 5837 5.04 %
Rwork0.2024 --
obs0.2043 115906 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.39 Å2 / Biso mean: 52.4739 Å2 / Biso min: 17.17 Å2
Refinement stepCycle: final / Resolution: 2.75→162.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15018 0 440 14 15472
Biso mean--55.11 32.39 -
Num. residues----1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915851
X-RAY DIFFRACTIONf_angle_d1.01421729
X-RAY DIFFRACTIONf_chiral_restr0.062393
X-RAY DIFFRACTIONf_plane_restr0.0072772
X-RAY DIFFRACTIONf_dihedral_angle_d13.6349079
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8747X-RAY DIFFRACTION7.118TORSIONAL
12B8747X-RAY DIFFRACTION7.118TORSIONAL
13C8747X-RAY DIFFRACTION7.118TORSIONAL
14D8747X-RAY DIFFRACTION7.118TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.78130.32852010.310536003801100
2.7813-2.8140.31631640.300536303794100
2.814-2.84830.3371860.302236243810100
2.8483-2.88440.35911720.298436503822100
2.8844-2.92230.34252050.289336003805100
2.9223-2.96230.33411780.274736323810100
2.9623-3.00470.33611950.259836283823100
3.0047-3.04950.31492190.261536123831100
3.0495-3.09720.32272050.257936213826100
3.0972-3.1480.30381700.248636403810100
3.148-3.20220.29061930.2536293822100
3.2022-3.26050.29931880.246836543842100
3.2605-3.32320.2942130.256635973810100
3.3232-3.3910.29552020.25536383840100
3.391-3.46480.26222060.221336343840100
3.4648-3.54540.23561940.207836303824100
3.5454-3.63410.27551760.202536813857100
3.6341-3.73230.21621930.187536373830100
3.7323-3.84220.20971960.180536583854100
3.8422-3.96620.22311770.176136753852100
3.9662-4.10790.2291930.179536703863100
4.1079-4.27240.19472050.155736693874100
4.2724-4.46690.18091780.151836933871100
4.4669-4.70240.17831950.144236853880100
4.7024-4.9970.17351970.152237073904100
4.997-5.38290.20452050.165137033908100
5.3829-5.92460.22061920.183837473939100
5.9246-6.78190.21432080.184537773985100
6.7819-8.54450.20662130.178537954008100
8.5445-162.94680.20012180.19383953417198
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)
12.13260.0279-0.36720.4575-0.12410.5189-0.01830.57670.0223-0.05070.0163-0.0707-0.0312-0.0753-0.00250.24020.04540.0410.4516-0.04510.404671.955878.1746159.3911
21.5867-1.24610.09751.72040.15850.6079-0.2766-0.22450.05650.47680.19560.0425-0.0525-0.04780.09040.41070.11280.02740.2986-0.03520.420624.88103.0388211.4227
31.4859-0.08380.10140.33730.12470.3864-0.04010.759-0.313-0.07360.14770.06740.08780.174-0.04180.3028-0.0021-0.08750.7112-0.14730.465525.919268.5053149.5183
40.9412-0.6938-0.01531.2625-0.07460.4415-0.3013-0.2732-0.32720.7330.37750.3693-0.1195-0.1779-0.02650.61930.21910.13870.43450.17230.515342.473859.2219221.1154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not (resname NDP or resname FAD or resname SO4 or resname HOH)A0
2X-RAY DIFFRACTION2chain B and not (resname NDP or resname FAD or resname SO4 or resname HOH)B0
3X-RAY DIFFRACTION3chain C and not (resname NDP or resname FAD or resname SO4 or resname HOH)C0
4X-RAY DIFFRACTION4chain D and not (resname NDP or resname FAD or resname SO4 or resname HOH)D0

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