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- PDB-3hdq: Crystal structure of UDP-galactopyranose mutase (oxidized form) i... -

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Basic information

Entry
Database: PDB / ID: 3hdq
TitleCrystal structure of UDP-galactopyranose mutase (oxidized form) in complex with substrate
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-galactopyranose mutase / Substrate and inhibitor
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 / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsPartha, S.K. / van Straaten, K.E. / Sanders, D.A.
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)470,93730
Polymers457,41810
Non-polymers13,51920
Water22,3571241
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
Buried area7390 Å2
ΔGint-32 kcal/mol
Surface area29320 Å2
MethodPISA
2
B: UDP-galactopyranose mutase
H: 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
Buried area7370 Å2
ΔGint-34 kcal/mol
Surface area29250 Å2
MethodPISA
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
Buried area7240 Å2
ΔGint-39 kcal/mol
Surface area29500 Å2
MethodPISA
4
D: UDP-galactopyranose mutase
J: 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
Buried area7170 Å2
ΔGint-37 kcal/mol
Surface area28980 Å2
MethodPISA
5
E: UDP-galactopyranose mutase
G: 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
Buried area7250 Å2
ΔGint-36 kcal/mol
Surface area29310 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50530 Å2
ΔGint-204 kcal/mol
Surface area132260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.020, 176.650, 220.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 10 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1241 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growpH: 6.5
Details: 0.1 M HEPES pH 6.5, 0.2 M LiCl, 28% PEG 6000, Microbatch

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9797 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.36→19.88 Å / Num. all: 204925 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 13.07

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Processing

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

1v0j


Resolution: 2.36→19.88 Å / SU ML: 0.13 / σ(F): 1.99 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 10667 5 %
Rwork0.1768 --
obs0.1793 213337 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.307 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 37.046 Å2
Baniso -1Baniso -2Baniso -3
1-1.923 Å2-0 Å20 Å2
2---1.935 Å2-0 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 2.36→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29744 0 890 1241 31875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731558
X-RAY DIFFRACTIONf_angle_d1.15243085
X-RAY DIFFRACTIONf_dihedral_angle_d19.45511611
X-RAY DIFFRACTIONf_chiral_restr0.0774510
X-RAY DIFFRACTIONf_plane_restr0.0055526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.38680.28663510.2226669X-RAY DIFFRACTION99
2.3868-2.41480.28333500.22216662X-RAY DIFFRACTION100
2.4148-2.44420.283510.21936657X-RAY DIFFRACTION100
2.4442-2.47510.28023520.2176694X-RAY DIFFRACTION100
2.4751-2.50760.25383520.20586678X-RAY DIFFRACTION100
2.5076-2.54190.27163520.20236699X-RAY DIFFRACTION100
2.5419-2.57810.29163530.20916710X-RAY DIFFRACTION100
2.5781-2.61650.3013520.21866691X-RAY DIFFRACTION100
2.6165-2.65730.27113530.20696693X-RAY DIFFRACTION100
2.6573-2.70080.27593530.20286716X-RAY DIFFRACTION100
2.7008-2.74720.27323540.19946716X-RAY DIFFRACTION100
2.7472-2.79710.25873550.20356749X-RAY DIFFRACTION100
2.7971-2.85070.27523540.21456727X-RAY DIFFRACTION100
2.8507-2.90870.26213530.19816717X-RAY DIFFRACTION100
2.9087-2.97180.28633560.20856749X-RAY DIFFRACTION100
2.9718-3.04070.26763540.20546727X-RAY DIFFRACTION100
3.0407-3.11640.26973540.21246725X-RAY DIFFRACTION100
3.1164-3.20030.27913540.20376729X-RAY DIFFRACTION100
3.2003-3.29410.25353550.19346745X-RAY DIFFRACTION100
3.2941-3.39990.22793560.1816765X-RAY DIFFRACTION100
3.3999-3.52080.21913560.16856773X-RAY DIFFRACTION100
3.5208-3.66090.22383550.17356742X-RAY DIFFRACTION100
3.6609-3.82640.22343590.16786811X-RAY DIFFRACTION100
3.8264-4.02660.19623570.15726782X-RAY DIFFRACTION100
4.0266-4.27650.18533570.14196797X-RAY DIFFRACTION100
4.2765-4.60290.15033580.12216802X-RAY DIFFRACTION100
4.6029-5.05920.16483590.12916825X-RAY DIFFRACTION100
5.0592-5.77550.19143620.14666866X-RAY DIFFRACTION100
5.7755-7.21820.18883640.15156923X-RAY DIFFRACTION100
7.2182-19.88180.16123760.13617131X-RAY DIFFRACTION100

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