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- PDB-2bi7: udp-galactopyranose mutase from Klebsiella pneumoniae oxidised FAD -

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Basic information

Entry
Database: PDB / ID: 2bi7
Titleudp-galactopyranose mutase from Klebsiella pneumoniae oxidised FAD
ComponentsUDP-GALACTOPYRANOSE MUTASE
KeywordsISOMERASE / 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 / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBeis, K. / Srikannathasan, V. / Naismith, J.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of Mycobacteria Tuberculosis and Klebsiella Pneumoniae Udp-Galactopyranose Mutase in the Oxidised State and Klebsiella Pneumoniae Udp-Galactopyranose Mutase in the (Active) Reduced State.
Authors: Beis, K. / Srikannathasan, V. / Liu, H. / Fullerton, S.W.B. / Bamford, V.A. / Sanders, D.A.R. / Whitfield, C. / Mcneil, M.R. / Naismith, J.H.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Udp-Galactopyranose Mutase Has a Novel Structure and Mechanism
Authors: Sanders, D.A. / Staines, A.G. / Mcmahon, S.A. / Mcneil, M.R. / Whitfield, C. / Naismith, J.H.
History
DepositionJan 20, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionMay 5, 2005ID: 1USJ
Revision 1.0May 5, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 25, 2015Group: Database references / Derived calculations / Structure summary
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: UDP-GALACTOPYRANOSE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2982
Polymers44,5121
Non-polymers7861
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)85.675, 85.675, 99.793
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein UDP-GALACTOPYRANOSE MUTASE


Mass: 44512.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / 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.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: INVOLVED IN THE CONVERSION OF UDP-GALP INTO UDP-GALF THROUGH A 2-KETO INTERMEDIATE

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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: 2.35 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.5
Details: 0.1M BIS-TRIS PH6.5, 50MM CACL2, 30% PEG550, pH 6.50

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→74.54 Å / Num. obs: 2160 / % possible obs: 98.1 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.12 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.3 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I8T

1i8t


Resolution: 2→74.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1293 5 %RANDOM
Rwork0.193 ---
obs0.195 24352 88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 53 140 3311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223260
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9594426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53123.952167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49315532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9471518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022527
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21429
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22210
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.51963
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02323082
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.62331554
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.394.51344
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 35
Rwork0.29 733
Refinement TLS params.Method: refined / Origin x: -12.4 Å / Origin y: 25.342 Å / Origin z: 11.421 Å
111213212223313233
T-0.0775 Å20.0515 Å20.0419 Å2-0.0039 Å2-0.0369 Å2---0.0651 Å2
L1.4028 °2-0.8536 °20.9652 °2-1.3837 °2-0.8216 °2--1.5392 °2
S0.1147 Å °0.28 Å °0.1048 Å °-0.1707 Å °-0.1156 Å °-0.1368 Å °0.1321 Å °0.2668 Å °0.0009 Å °

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