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- PDB-3kyb: Structure of UDP-galactopyranose mutase bound to flavin mononucleotide -

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Basic information

Entry
Database: PDB / ID: 3kyb
TitleStructure of UDP-galactopyranose mutase bound to flavin mononucleotide
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
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 / FLAVIN MONONUCLEOTIDE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGruber, T.D. / Dimond, M.C. / Kiessling, L.L. / Forest, K.T.
CitationJournal: To be Published
Title: Structure of UDP-galactopyranose mutase bound to flavin mononucleotide
Authors: Gruber, T.D. / Dimond, M.C. / Kiessling, L.L. / Forest, K.T.
History
DepositionDec 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: 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)93,8728
Polymers90,4762
Non-polymers3,3966
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-9 kcal/mol
Surface area34400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.8, 93.8, 128.8
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
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
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 PH 7.0 WERE COMBINED WITH 1.5 MICROLITERS WELL SOLUTION (85 MM AMMONIUM ACETATE, 42 MM TRI-SODIUM CITRATE, 12.3% PEG 4000, 7. ...Details: DROPS CONTAINING 1.5 MICROLITERS 5 MG/ML PROTEIN IN 20 MM HEPES PH 7.0 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. CRYSTAL WAS THEN SOAKED IN A SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS AND 23 MM FLAVIN MONONUCLEOTIDE (24HRS). CRYSTAL WAS BRIEFLY SOAKED (20 SECONDS) IN A SOLUTION OF 53% QIAGEN CRYOS SUITE CONDITION #87 WITH 15 MM L-CYS, 30% METHANOL, 10 MM FLAVIN MONONUCLEOTIDE PRIOR TO VITRIFICATION, 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: 0.97857 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: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 49496 / Num. obs: 49472 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 39.2 Å2 / Rsym value: 0.093 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 7.2 / Num. unique all: 4912 / Rsym value: 0.286 / % 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: PDB ENTRY 3GF4

3gf4


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.245 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2499 5.1 %RANDOM
Rwork0.183 ---
all0.185 46879 --
obs0.185 46820 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.197 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 230 294 6751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226642
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9819037
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13724.072334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.464151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91534
X-RAY DIFFRACTIONr_chiral_restr0.140.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215116
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_it1.2291.53800
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21526150
X-RAY DIFFRACTIONr_scbond_it3.46932842
X-RAY DIFFRACTIONr_scangle_it5.4034.52887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 178 -
Rwork0.207 3388 -
obs-3388 98.67 %

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