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- PDB-3gf4: Structure of UDP-galactopyranose mutase bound to UDP-glucose -

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Basic information

Entry
Database: PDB / ID: 3gf4
TitleStructure of UDP-galactopyranose mutase bound to UDP-glucose
ComponentsUDP-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
FLAVIN-ADENINE DINUCLEOTIDE / URIDINE-5'-MONOPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGruber, T.D. / Borrok, M.J. / Kiessling, L.L. / Forest, K.T.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Ligand binding and substrate discrimination by UDP-galactopyranose mutase.
Authors: Gruber, T.D. / Borrok, M.J. / Westler, W.M. / Forest, K.T. / Kiessling, L.L.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 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 1.4Sep 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,9376
Polymers90,4762
Non-polymers2,4624
Water3,513195
1


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


Theoretical massNumber of molelcules
Total (without water)46,3483
Polymers45,2381
Non-polymers1,1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5903
Polymers45,2381
Non-polymers1,3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.951, 93.951, 130.259
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 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 / 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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5 mg/mL protein, 85 mM ammonium acetate, 42 mM tri-sodium citrate, 12.3% PEG 4000, 7.5% glycerol, 15 mM L-cysteine, 5 mM UDP-Glc, 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: 14-ID-B / Wavelength: 0.9002 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 27, 2006 / Details: rhodium coated toroidal mirror
RadiationMonochromator: Double diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 41757 / Num. obs: 41161 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 53.9 Å2 / Rsym value: 0.11 / Χ2: 1.536 / Net I/σ(I): 14.831
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 4042 / Rsym value: 0.366 / Χ2: 1.634 / % possible all: 97

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BI8

2bi8


Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.252 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2064 5 %RANDOM
Rwork0.192 ---
all0.194 41510 --
obs0.194 40988 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.93 Å2 / Biso mean: 45.792 Å2 / Biso min: 26.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20 Å2
2---1.79 Å20 Å2
3---3.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.245 Å0.348 Å
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6238 0 163 195 6596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226582
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9678945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22524.072334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.612151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5121534
X-RAY DIFFRACTIONr_chiral_restr0.1170.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025072
X-RAY DIFFRACTIONr_nbd_refined0.2250.22889
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2309
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.211
X-RAY DIFFRACTIONr_mcbond_it1.4661.53917
X-RAY DIFFRACTIONr_mcangle_it1.69826166
X-RAY DIFFRACTIONr_scbond_it2.85733222
X-RAY DIFFRACTIONr_scangle_it3.9744.52779
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 153 -
Rwork0.256 2820 -
all-2973 -
obs-2820 96.78 %

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