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- PDB-3int: Structure of UDP-galactopyranose mutase bound to UDP-galactose (r... -

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Basic information

Entry
Database: PDB / ID: 3int
TitleStructure of UDP-galactopyranose mutase bound to UDP-galactose (reduced)
ComponentsProbable UDP-galactopyranose mutase
KeywordsISOMERASE / Flavoenzyme / protein-ligand complex / carbohydrate biosynthesis / FAD / Flavoprotein / Lipopolysaccharide biosynthesis
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / O antigen biosynthetic process / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / GALACTOSE-URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsGruber, T.D. / Kiessling, L.L. / Forest, K.T.
CitationJournal: Biochemistry / Year: 2009
Title: X-ray crystallography reveals a reduced substrate complex of UDP-galactopyranose mutase poised for covalent catalysis by flavin .
Authors: Gruber, T.D. / Westler, W.M. / Kiessling, L.L. / Forest, K.T.
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable UDP-galactopyranose mutase
B: Probable UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0216
Polymers90,4762
Non-polymers2,5464
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4303
Polymers45,2381
Non-polymers1,1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Probable UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5923
Polymers45,2381
Non-polymers1,3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.078, 94.078, 129.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Probable UDP-galactopyranose mutase


Mass: 45237.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal Arg384 was altered to glycine during cloning, and six histidine residues were engineered on the C-terminus as a tag.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 01 (ATCC 13882) / Gene: glf, rfbD / Plasmid: pGEM-Teasy / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48485, UDP-galactopyranose mutase
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE ARE VERY CONSERVATIVE MUTATIONS FROM THE PUBLISHED SEQUENCE. THEY REFLECT SEQUENCE ...THESE ARE VERY CONSERVATIVE MUTATIONS FROM THE PUBLISHED SEQUENCE. THEY REFLECT SEQUENCE DIFFERENCES IN THE ISOLATE THAT OUR CLONED DNA CAME FROM RATHER THAN ERRORS IN THE STRUCTURE OR THE PDB FILE

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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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Drops containing 1.5 microliters 5 mg/mL protein in 20 mM HEPES were combined with 1.5 microliters well solution (85 mM ammonium acetate, 42 mM tri-sodium citrate, 12.3% PEG 4000, 7.5% ...Details: Drops containing 1.5 microliters 5 mg/mL protein in 20 mM HEPES were combined with 1.5 microliters well solution (85 mM ammonium acetate, 42 mM tri-sodium citrate, 12.3% PEG 4000, 7.5% glycerol, 15 mM L-cysteine, 5 mM UDP-Glc) for 1-2 weeks. Crystals were then soaked in a solution of 53% Qiagen Cryos Suite Condition #87 with 15 mM L-cys, 30% methanol, 90 mM UDP-Galp (24hrs). Crystals were then soaked in a solution of 53% Qiagen Cryos Suite Condition #87 with 15 mM L-cys, 30% methanol, 90 mM UDP-Galp plus 100 mM sodium dithionite (3 min), pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2008 / Details: Beryllium lens
RadiationMonochromator: C(111) diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 38556 / Num. obs: 38510 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.107 / Net I/σ(I): 15
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 6.7 / Rsym value: 0.329 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GF4

3gf4


Resolution: 2.51→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.461 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1925 5 %RANDOM
Rwork0.19377 ---
obs0.19643 36538 99.47 %-
all-36733 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.795 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---1.2 Å20 Å2
3---2.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.267 Å0.391 Å
Refinement stepCycle: LAST / Resolution: 2.51→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 0 167 200 6527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9818832
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39524.03330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.753151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8731534
X-RAY DIFFRACTIONr_chiral_restr0.1210.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215005
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9831.53761
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8626075
X-RAY DIFFRACTIONr_scbond_it2.75232740
X-RAY DIFFRACTIONr_scangle_it4.4694.52757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 122 -
Rwork0.277 2530 -
obs--93.68 %

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