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- PDB-4mo2: Crystal Structure of UDP-N-acetylgalactopyranose mutase from Camp... -

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Basic information

Entry
Database: PDB / ID: 4mo2
TitleCrystal Structure of UDP-N-acetylgalactopyranose mutase from Campylobacter jejuni
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-N-acetylgalactopyranose mutase / UNGM / capsular polysaccharides / bifunctional / drug target / FAD
Function / homology
Function and homology information


UDP-galactopyranose mutase / 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 / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / AMMONIUM ION / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDalrymple, S.A. / Protsko, C. / Poulin, M.B. / Lowary, T.L. / Sanders, D.A.R.
CitationJournal: Chembiochem / Year: 2014
Title: Specificity of a UDP-GalNAc Pyranose-Furanose Mutase: A Potential Therapeutic Target for Campylobacter jejuni Infections.
Authors: Poulin, M.B. / Shi, Y. / Protsko, C. / Dalrymple, S.A. / Sanders, D.A. / Pinto, B.M. / Lowary, T.L.
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: UDP-galactopyranose mutase
A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,99210
Polymers87,0072
Non-polymers1,9868
Water13,998777
1
A: UDP-galactopyranose mutase
hetero molecules

B: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,99210
Polymers87,0072
Non-polymers1,9868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area5060 Å2
ΔGint-54 kcal/mol
Surface area33370 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-42 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.420, 116.150, 165.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein UDP-galactopyranose mutase


Mass: 43503.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: 11168 / Gene: Cj1439c, glf / Plasmid: pWM1007 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q0P8H5, UDP-galactopyranose mutase

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Non-polymers , 6 types, 785 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 277 K / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M tri-Sodium citrate pH 5.6, 25%(w/v) PEG 4000, microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2010
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→47.51 Å / Num. all: 63966 / Num. obs: 63966 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.11 % / Biso Wilson estimate: 21.51 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.832.51310774619100
2.05-2.110.6863.04312644598100
2.11-2.170.5563.77301954390100
2.17-2.240.4914.31299264322100
2.24-2.310.4364.89292474170100
2.31-2.390.3815.59286094037100
2.39-2.480.3276.38276183884100
2.48-2.580.2857.38274403800100
2.58-2.70.2448.66264933647100
2.7-2.830.20810251973432100
2.83-2.980.16612.2824187327999.9
2.98-3.160.13415.12232643141100
3.16-3.380.09819.78218262952100
3.38-3.650.07224.96203052755100
3.65-40.05829.82188262566100
4-4.470.04734.63168712325100
4.47-5.160.04436.02147842051100
5.16-6.320.05429.68126381772100
6.32-8.940.04533.7897561398100
8.940.03441.98525482899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.51 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8788 / SU ML: 0.21 / σ(F): 1.36 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 3199 5 %RANDOM
Rwork0.1712 ---
obs0.1733 63959 99.97 %-
all-63959 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.7 Å2 / Biso mean: 26.1989 Å2 / Biso min: 5.75 Å2
Refinement stepCycle: LAST / Resolution: 2→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 130 777 6990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026408
X-RAY DIFFRACTIONf_angle_d0.678675
X-RAY DIFFRACTIONf_chiral_restr0.051880
X-RAY DIFFRACTIONf_plane_restr0.0021092
X-RAY DIFFRACTIONf_dihedral_angle_d14.3232423
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.02990.33631360.247825792715
2.0299-2.06160.2591360.231725792715
2.0616-2.09540.28661390.219126402779
2.0954-2.13150.23521360.211525862722
2.1315-2.17030.2641370.209526072744
2.1703-2.2120.26591380.202426232761
2.212-2.25720.29251370.194725922729
2.2572-2.30630.24741380.188426232761
2.3063-2.35990.23911370.187726062743
2.3599-2.41890.23311390.183326392778
2.4189-2.48430.23061360.175425852721
2.4843-2.55740.22321400.178226542794
2.5574-2.640.23891360.17125942730
2.64-2.73430.21861400.17526522792
2.7343-2.84380.25661380.174626362774
2.8438-2.97320.21311390.174126392778
2.9732-3.12990.18841380.165126212759
3.1299-3.32590.18671400.1626572797
3.3259-3.58270.21410.152126742815
3.5827-3.9430.17381400.138126672807
3.943-4.51320.16341430.133427042847
4.5132-5.68470.18741430.151327212864
5.6847-47.52510.181520.187728823034

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