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- PDB-5hhf: Crystal structure of Aspergillus fumigatus UDP-Galactopyranose mu... -

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Basic information

Entry
Database: PDB / ID: 5hhf
TitleCrystal structure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant H63A with covalent FAD-Galactopyranose and bound UDP
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / NUCLEOTIDE BINDING / MUTASE / FLAVIN ADENINE DINUCLEOTIDE BINDING / covalent reaction intermediate
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
Chem-62F / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / MESO-ERYTHRITOL / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsTanner, J.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM094469 United States
National Science Foundation (NSF, United States)CHE-1506206 United States
CitationJournal: Biochemistry / Year: 2016
Title: In Crystallo Capture of a Covalent Intermediate in the UDP-Galactopyranose Mutase Reaction.
Authors: Mehra-Chaudhary, R. / Dai, Y. / Sobrado, P. / Tanner, J.J.
History
DepositionJan 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 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
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)233,97824
Polymers228,2464
Non-polymers5,73220
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-54 kcal/mol
Surface area72450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.515, 217.515, 319.800
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 (resseq 3:40 or (resid 41 and (name...
21(chain B and (resseq 3:59 or (resid 60 and (name...
31(chain C and (resseq 3:40 or (resid 41 and (name...
41(chain D and (resseq 3:59 or (resid 60 and (name...

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
UDP-galactopyranose mutase /


Mass: 57061.422 Da / Num. of mol.: 4 / Mutation: H63A
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 , 6 types, 760 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MRY / MESO-ERYTHRITOL / Erythritol


Mass: 122.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O4
#4: Chemical ChemComp-62F / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-7,8-dimethyl-2,4-bis(oxidanyl)benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate


Mass: 949.706 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C33H45N9O20P2
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 74.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.6 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: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→61.61 Å / Num. obs: 196082 / % possible obs: 100 % / Redundancy: 21.1 % / Biso Wilson estimate: 32.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.045 / Net I/σ(I): 15.1 / Num. measured all: 4132787
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3420.51.4532.519656295800.8140.329100
12.6-61.6118.90.04438.52639114000.9990.0199

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Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3uth

3uth


Resolution: 2.3→61.61 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 3848 1.96 %
Rwork0.1845 192063 -
obs0.1851 195911 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.55 Å2 / Biso mean: 39.5653 Å2 / Biso min: 18.74 Å2
Refinement stepCycle: final / Resolution: 2.3→61.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15448 0 366 740 16554
Biso mean--54.07 38.78 -
Num. residues----2015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716210
X-RAY DIFFRACTIONf_angle_d0.94522174
X-RAY DIFFRACTIONf_chiral_restr0.0582453
X-RAY DIFFRACTIONf_plane_restr0.0062849
X-RAY DIFFRACTIONf_dihedral_angle_d13.0099452
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8830X-RAY DIFFRACTION6.896TORSIONAL
12B8830X-RAY DIFFRACTION6.896TORSIONAL
13C8830X-RAY DIFFRACTION6.896TORSIONAL
14D8830X-RAY DIFFRACTION6.896TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.32910.3521360.270470087144
2.3291-2.35980.26371270.261170477174
2.3598-2.39210.281300.254170027132
2.3921-2.42630.30951540.243370177171
2.4263-2.46250.25821330.233470467179
2.4625-2.5010.25411680.222870267194
2.501-2.5420.27961410.227770257166
2.542-2.58580.25991310.222370447175
2.5858-2.63280.25441430.219170627205
2.6328-2.68350.25551420.213670297171
2.6835-2.73820.26281420.215970367178
2.7382-2.79780.23861500.213470597209
2.7978-2.86290.27471470.205770887235
2.8629-2.93440.23441490.209570527201
2.9344-3.01380.23681500.201170747224
3.0138-3.10250.22451300.206270817211
3.1025-3.20260.24731400.213571037243
3.2026-3.31710.23821470.206870727219
3.3171-3.44990.20771470.196371297276
3.4499-3.60690.23691080.181471357243
3.6069-3.7970.19371350.16771477282
3.797-4.03480.17971490.156471747323
4.0348-4.34630.15671410.136971737314
4.3463-4.78350.14791420.124172067348
4.7835-5.47530.15811410.140372537394
5.4753-6.89690.21191550.170373317486
6.8969-61.63680.16541700.164376447814
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)
11.0535-0.0585-0.2770.04010.09310.3234-0.0140.23610.015-0.048-0.0263-0.11290.0226-0.0110.0350.21430.02790.05380.37120.02090.391271.635377.5921159.9478
20.4285-0.4114-0.01730.7889-0.08470.3965-0.0955-0.09080.03250.21540.05490.062-0.0059-0.02460.04270.28210.05320.02090.224-0.02990.287624.6036103.1147211.9352
31.04560.0102-0.08220.3218-0.02360.5721-0.0170.4285-0.2297-0.11080.04890.00460.09660.0426-0.0280.21980.0089-0.04070.4389-0.09630.312625.744367.7951150.1223
40.5335-0.4779-0.08860.94350.0850.5205-0.115-0.1604-0.16060.36230.13980.19030.0121-0.0512-0.0180.35150.08280.05080.26810.08910.310142.1359.6579222.1907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not (resname FDA)A0
2X-RAY DIFFRACTION2chain B and not (resname FDA)B0
3X-RAY DIFFRACTION3chain C and not (resname FDA)C0
4X-RAY DIFFRACTION4chain D and not (resname FDA)D0

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