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- PDB-2bi8: udp-galactopyranose mutase from Klebsiella pneumoniae with reduced FAD -

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Basic information

Entry
Database: PDB / ID: 2bi8
Titleudp-galactopyranose mutase from Klebsiella pneumoniae with reduced 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: 2.35 Å
AuthorsBeis, K. / Srikannathasan, V. / Naismith, J.H.
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
Revision 1.0May 5, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jan 31, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line ..._citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)85.997, 85.997, 100.809
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 BL21(DE3) (bacteria) / 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.: 126 / 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: Nov 25, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→27.12 Å / Num. obs: 18331 / % possible obs: 99.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 99.1

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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: 2.35→27.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 914 5 %RANDOM
Rwork0.187 ---
obs0.19 17405 99.5 %-
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: 62.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0.51 Å20 Å2
2---1.02 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.35→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 53 126 3297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223260
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.231.964426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37523.952167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83615532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9851518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022531
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21453
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22187
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4811.51952
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85723082
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.29531510
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9924.51344
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: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 57
Rwork0.276 1265
Refinement TLS params.Method: refined / Origin x: -28.302 Å / Origin y: -1.628 Å / Origin z: -11.668 Å
111213212223313233
T-0.0388 Å20.087 Å2-0.0518 Å2--0.0233 Å20.0109 Å2---0.1545 Å2
L2.3705 °2-0.6021 °2-1.3712 °2-0.8621 °20.4256 °2--1.6918 °2
S-0.2563 Å °-0.3904 Å °-0.1721 Å °0.2298 Å °0.1705 Å °-0.0024 Å °0.1692 Å °0.3295 Å °0.0858 Å °

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