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- PDB-3he3: Crystal Structure of UDP-galactopyranose mutase in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 3he3
TitleCrystal Structure of UDP-galactopyranose mutase in complex with UDP
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-galactopyranose mutase / inhibitor / UDP
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 / 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)469,31530
Polymers457,41810
Non-polymers11,89720
Water19,6721092
1
E: UDP-galactopyranose mutase
G: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8636
Polymers91,4842
Non-polymers2,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-33 kcal/mol
Surface area29580 Å2
MethodPISA
2
A: UDP-galactopyranose mutase
I: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8636
Polymers91,4842
Non-polymers2,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-31 kcal/mol
Surface area29840 Å2
MethodPISA
3
B: UDP-galactopyranose mutase
H: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8636
Polymers91,4842
Non-polymers2,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-33 kcal/mol
Surface area29590 Å2
MethodPISA
4
C: UDP-galactopyranose mutase
F: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8636
Polymers91,4842
Non-polymers2,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-36 kcal/mol
Surface area29370 Å2
MethodPISA
5
D: UDP-galactopyranose mutase
J: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8636
Polymers91,4842
Non-polymers2,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-34 kcal/mol
Surface area29510 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47660 Å2
ΔGint-191 kcal/mol
Surface area133980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.050, 176.874, 222.920
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 / Plasmid: pEHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: Q9RYF1, UDP-galactopyranose mutase
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#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.: 1092 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5
Details: 0.1 M HEPES, 0.2 M LiCl and 28% PEG 6000, pH 6.5, Microbatch, temperature 295K

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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: Mar 5, 2009
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.4→39.88 Å / Num. obs: 204114 / % possible obs: 98.9 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.182 / Rsym value: 0.182 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.5 / Num. unique all: 66447 / Rsym value: 0.598 / % possible all: 93.1

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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→39.88 Å / SU ML: -0 / σ(F): 1.34 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 10270 5.03 %
Rwork0.2085 --
obs0.2108 203985 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.776 Å2 / ksol: 0.354 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29678 0 780 1092 31550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431331
X-RAY DIFFRACTIONf_angle_d0.83842754
X-RAY DIFFRACTIONf_dihedral_angle_d17.79511160
X-RAY DIFFRACTIONf_chiral_restr0.0564451
X-RAY DIFFRACTIONf_plane_restr0.0035503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.41393170.38475885X-RAY DIFFRACTION91
2.4273-2.45580.40972930.37646065X-RAY DIFFRACTION93
2.4558-2.48580.39093040.36736128X-RAY DIFFRACTION95
2.4858-2.51720.393470.36296288X-RAY DIFFRACTION97
2.5172-2.55030.40283410.34046290X-RAY DIFFRACTION97
2.5503-2.58530.38053070.33816358X-RAY DIFFRACTION98
2.5853-2.62220.34633240.30936410X-RAY DIFFRACTION98
2.6222-2.66130.36943370.31236417X-RAY DIFFRACTION99
2.6613-2.70290.34723600.29256409X-RAY DIFFRACTION99
2.7029-2.74720.3443090.27046525X-RAY DIFFRACTION100
2.7472-2.79460.3073410.25946497X-RAY DIFFRACTION100
2.7946-2.84540.31813500.26356500X-RAY DIFFRACTION100
2.8454-2.90010.31613800.25346425X-RAY DIFFRACTION100
2.9001-2.95930.32133290.25016526X-RAY DIFFRACTION100
2.9593-3.02360.31343230.24936530X-RAY DIFFRACTION100
3.0236-3.09390.31493460.24176525X-RAY DIFFRACTION100
3.0939-3.17120.28133680.22376463X-RAY DIFFRACTION100
3.1712-3.25690.27913500.21626506X-RAY DIFFRACTION100
3.2569-3.35270.25523320.20926547X-RAY DIFFRACTION100
3.3527-3.46090.23163450.18616516X-RAY DIFFRACTION100
3.4609-3.58450.24553670.17386493X-RAY DIFFRACTION100
3.5845-3.72790.22113300.17196571X-RAY DIFFRACTION100
3.7279-3.89750.20243270.1576552X-RAY DIFFRACTION100
3.8975-4.10280.19563370.14866583X-RAY DIFFRACTION100
4.1028-4.35950.17923420.13496590X-RAY DIFFRACTION100
4.3595-4.69560.1733650.12846538X-RAY DIFFRACTION100
4.6956-5.16730.18063620.13276626X-RAY DIFFRACTION100
5.1673-5.91290.2093670.16046609X-RAY DIFFRACTION100
5.9129-7.44170.21213650.16826701X-RAY DIFFRACTION100
7.4417-39.88720.18824050.18196642X-RAY DIFFRACTION97

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