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

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Basic information

Entry
Database: PDB / ID: 5vwu
TitleCrystal structure of oxidized Aspergillus fumigatus UDP-galactopyranose mutase complexed with NADH
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
FLAVIN-ADENINE DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 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: 4GDD
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

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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)234,23623
Polymers228,5144
Non-polymers5,72219
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-277 kcal/mol
Surface area73420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.247, 218.247, 318.004
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 4 through 5 or (resid 6...
21(chain B and (resid 4 through 5 or (resid 6...
31(chain C and (resid 4 through 9 or (resid 10...
41(chain D and (resid 4 through 59 or (resid 60...

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
11PROPROASPASP(chain A and (resid 4 through 5 or (resid 6...AA4 - 57 - 8
12ILEILEILEILE(chain A and (resid 4 through 5 or (resid 6...AA69
13HISHISLYSLYS(chain A and (resid 4 through 5 or (resid 6...AA3 - 5066 - 509
14HISHISLYSLYS(chain A and (resid 4 through 5 or (resid 6...AA3 - 5066 - 509
15HISHISLYSLYS(chain A and (resid 4 through 5 or (resid 6...AA3 - 5066 - 509
16HISHISLYSLYS(chain A and (resid 4 through 5 or (resid 6...AA3 - 5066 - 509
21PROPROASPASP(chain B and (resid 4 through 5 or (resid 6...BB4 - 57 - 8
22ILEILEILEILE(chain B and (resid 4 through 5 or (resid 6...BB69
23HISHISSERSER(chain B and (resid 4 through 5 or (resid 6...BB3 - 5076 - 510
24HISHISSERSER(chain B and (resid 4 through 5 or (resid 6...BB3 - 5076 - 510
25HISHISSERSER(chain B and (resid 4 through 5 or (resid 6...BB3 - 5076 - 510
26HISHISSERSER(chain B and (resid 4 through 5 or (resid 6...BB3 - 5076 - 510
31PROPROASPASP(chain C and (resid 4 through 9 or (resid 10...CC4 - 97 - 12
32VALVALVALVAL(chain C and (resid 4 through 9 or (resid 10...CC1013
33PROPROLYSLYS(chain C and (resid 4 through 9 or (resid 10...CC4 - 5067 - 509
34PROPROLYSLYS(chain C and (resid 4 through 9 or (resid 10...CC4 - 5067 - 509
35PROPROLYSLYS(chain C and (resid 4 through 9 or (resid 10...CC4 - 5067 - 509
36PROPROLYSLYS(chain C and (resid 4 through 9 or (resid 10...CC4 - 5067 - 509
41PROPROASPASP(chain D and (resid 4 through 59 or (resid 60...DD4 - 597 - 62
42VALVALVALVAL(chain D and (resid 4 through 59 or (resid 60...DD6063
43HISHISLYSLYS(chain D and (resid 4 through 59 or (resid 60...DD3 - 5066 - 509
44HISHISLYSLYS(chain D and (resid 4 through 59 or (resid 60...DD3 - 5066 - 509
45HISHISLYSLYS(chain D and (resid 4 through 59 or (resid 60...DD3 - 5066 - 509
46HISHISLYSLYS(chain D and (resid 4 through 59 or (resid 60...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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 74.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
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→162.476 Å / Num. all: 115207 / Num. obs: 115207 / % possible obs: 99.6 % / Redundancy: 8.5 % / Biso Wilson estimate: 51.21 Å2 / Rpim(I) all: 0.054 / Rrim(I) all: 0.168 / Rsym value: 0.158 / Net I/av σ(I): 4.6 / Net I/σ(I): 10.9 / Num. measured all: 982507
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.75-2.97.91.2160.60.4291.2971.21699.9
2.9-3.078.10.7141.10.250.7620.714100
3.07-3.298.30.4211.80.1460.4480.42199.9
3.29-3.558.60.2662.90.0910.2830.26699.8
3.55-3.898.80.1644.60.0560.1740.16499.6
3.89-4.3590.1196.20.0410.1270.11999.3
4.35-5.0290.0947.50.0320.10.09499.5
5.02-6.158.90.0848.40.0280.090.08499.3
6.15-8.78.90.06110.80.020.0650.06199.2
8.7-162.4768.40.04213.50.0150.0450.04297.5

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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→28.586 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.72
RfactorNum. reflection% reflection
Rfree0.2273 5791 5.04 %
Rwork0.1941 --
obs0.1958 114952 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.68 Å2 / Biso mean: 55.1156 Å2 / Biso min: 24.57 Å2
Refinement stepCycle: final / Resolution: 2.75→28.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15207 0 365 19 15591
Biso mean--59.4 39.14 -
Num. residues----1995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815969
X-RAY DIFFRACTIONf_angle_d1.01321848
X-RAY DIFFRACTIONf_chiral_restr0.062402
X-RAY DIFFRACTIONf_plane_restr0.0072793
X-RAY DIFFRACTIONf_dihedral_angle_d13.1569203
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8921X-RAY DIFFRACTION7.903TORSIONAL
12B8921X-RAY DIFFRACTION7.903TORSIONAL
13C8921X-RAY DIFFRACTION7.903TORSIONAL
14D8921X-RAY DIFFRACTION7.903TORSIONAL
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 (%)
2.75-2.78120.30941970.298836103807100
2.7812-2.81390.30841690.271836183787100
2.8139-2.84820.30441800.273335983778100
2.8482-2.88420.31021840.261336193803100
2.8842-2.92210.32291890.263436233812100
2.9221-2.96210.3131900.263635993789100
2.9621-3.00440.27991910.256736083799100
3.0044-3.04920.33062250.260835803805100
3.0492-3.09680.2811910.251436103801100
3.0968-3.14750.30061800.247636223802100
3.1475-3.20170.25981890.235136163805100
3.2017-3.25980.26111850.222536363821100
3.2598-3.32250.27352100.2335893799100
3.3225-3.39020.28682080.234736013809100
3.3902-3.46380.24252010.228336373838100
3.4638-3.54420.231960.202135983794100
3.5442-3.63270.26421710.19263651382299
3.6327-3.73070.22531970.180635943791100
3.7307-3.84020.19661890.17433629381899
3.8402-3.96380.20531750.173653382899
3.9638-4.10510.20781930.16483624381799
4.1051-4.2690.17042020.14653621382399
4.269-4.46260.16561740.14163654382899
4.4626-4.69690.17621900.139336583848100
4.6969-4.98970.18711970.15323679387699
4.9897-5.37260.18732030.16393655385899
5.3726-5.9090.23271890.18313705389499
5.909-6.75420.21492080.19213713392199
6.7542-8.47260.20892100.1893734394499
8.4726-28.58750.20212080.18893827403596
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)
11.8852-0.0456-0.28650.4916-0.22570.552-0.01070.59260.0103-0.07420.0066-0.084-0.0197-0.0864-0.00210.27780.04650.03760.5536-0.05670.373371.662478.172158.4526
21.2943-0.9497-0.01031.35470.07420.4296-0.2138-0.21010.02040.44180.16070.0816-0.0641-0.01670.04790.48020.11530.03660.3567-0.02580.370724.8483103.1868210.9048
31.7059-0.05020.00940.34140.09280.5215-0.01140.7494-0.3925-0.10080.11690.05080.09370.1322-0.06860.35660.0125-0.08350.7307-0.15410.43925.651768.3828149.0481
40.8584-0.7221-0.13351.4138-0.03950.4327-0.2771-0.3074-0.31150.71690.36960.3952-0.0516-0.1203-0.02350.64190.19530.12260.48260.16550.470242.344459.4884220.4871
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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