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- PDB-3hdy: Crystal Structure of UDP-galactopyranose mutase (reduced form) in... -

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Basic information

Entry
Database: PDB / ID: 3hdy
TitleCrystal Structure of UDP-galactopyranose mutase (reduced form) in complex with substrate
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-galactopyranose mutase / reduced form / substrate
Function / homology
Function and homology information


UDP-galactopyranose mutase activity / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
UDP-galactopyranose mutase / UDP-galactopyranose mutase, C-terminal / UDP-galactopyranose mutase / NAD(P)-binding Rossmann-like domain / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPartha, S.K. / van Straaten, K.E. / Sanders, D.A.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP.
Authors: Partha, S.K. / van Straaten, K.E. / Sanders, D.A.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
E: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
G: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
I: UDP-galactopyranose mutase
J: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,94330
Polymers457,41810
Non-polymers13,52520
Water10,016556
1
A: UDP-galactopyranose mutase
I: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1876
Polymers91,4842
Non-polymers2,7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1896
Polymers91,4842
Non-polymers2,7064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1876
Polymers91,4842
Non-polymers2,7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-galactopyranose mutase
J: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1896
Polymers91,4842
Non-polymers2,7064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: UDP-galactopyranose mutase
G: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1896
Polymers91,4842
Non-polymers2,7064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50170 Å2
ΔGint-202 kcal/mol
Surface area130260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.820, 174.628, 218.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details5 homodimers

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Components

#1: Protein
UDP-galactopyranose mutase


Mass: 45741.824 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_A0367, DR_AO367 / Plasmid: pEHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: Q9RYF1, UDP-galactopyranose mutase
#2: Chemical
ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5
Details: 0.1 M HEPES pH 6.5, 0.2 M LiCl and 28 % PEG 6000, Microbatch, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9797 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.4→39.94 Å / Num. obs: 189435 / % possible obs: 95.8 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 4.7 % / Rmerge(I) obs: 0.187 / Rsym value: 0.187 / Net I/σ(I): 5.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.34 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.7 / Num. unique all: 78255 / % possible all: 92.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1V0J

1v0j


Resolution: 2.4→39.94 Å / SU ML: -0 / σ(F): 1.34 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2801 9505 5.02 %
Rwork0.2355 --
obs0.2377 189334 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.28 Å2 / ksol: 0.393 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29444 0 890 556 30890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331240
X-RAY DIFFRACTIONf_angle_d0.74942655
X-RAY DIFFRACTIONf_dihedral_angle_d19.08111684
X-RAY DIFFRACTIONf_chiral_restr0.0494404
X-RAY DIFFRACTIONf_plane_restr0.0045484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.40723010.37355612X-RAY DIFFRACTION91
2.4273-2.45580.39613160.35755754X-RAY DIFFRACTION92
2.4558-2.48580.37892640.34155769X-RAY DIFFRACTION93
2.4858-2.51720.39283190.33665812X-RAY DIFFRACTION94
2.5172-2.55040.37033140.33525795X-RAY DIFFRACTION94
2.5504-2.58530.36853070.33955837X-RAY DIFFRACTION94
2.5853-2.62220.36693120.31115880X-RAY DIFFRACTION94
2.6222-2.66130.34173380.29665852X-RAY DIFFRACTION95
2.6613-2.70290.33832970.29025922X-RAY DIFFRACTION95
2.7029-2.74720.32582880.28555924X-RAY DIFFRACTION95
2.7472-2.79460.33983370.27945930X-RAY DIFFRACTION96
2.7946-2.84540.35113000.27185977X-RAY DIFFRACTION96
2.8454-2.90010.32393180.25676021X-RAY DIFFRACTION96
2.9001-2.95930.29713380.24855998X-RAY DIFFRACTION97
2.9593-3.02360.34183000.25946033X-RAY DIFFRACTION97
3.0236-3.09390.31233630.24996015X-RAY DIFFRACTION97
3.0939-3.17130.31343030.23556066X-RAY DIFFRACTION97
3.1713-3.2570.28453250.23466062X-RAY DIFFRACTION97
3.257-3.35280.30653090.23696088X-RAY DIFFRACTION97
3.3528-3.46090.26273240.21366057X-RAY DIFFRACTION97
3.4609-3.58450.27873240.21616096X-RAY DIFFRACTION97
3.5845-3.7280.30563200.25436125X-RAY DIFFRACTION98
3.728-3.89750.31113150.2556126X-RAY DIFFRACTION98
3.8975-4.10280.23813170.19896129X-RAY DIFFRACTION98
4.1028-4.35950.21523480.1726147X-RAY DIFFRACTION98
4.3595-4.69570.23933210.20276160X-RAY DIFFRACTION98
4.6957-5.16730.18853310.16716166X-RAY DIFFRACTION98
5.1673-5.9130.243170.19126198X-RAY DIFFRACTION97
5.913-7.44180.22813190.19326184X-RAY DIFFRACTION96
7.4418-39.94220.19143200.17366094X-RAY DIFFRACTION92

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