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- PDB-1v0j: Udp-galactopyranose mutase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1v0j
TitleUdp-galactopyranose mutase from Mycobacterium tuberculosis
ComponentsUDP-GALACTOPYRANOSE MUTASE
KeywordsISOMERASE / MUTASE / FLAVOPROTEIN
Function / homology
Function and homology information


UDP-galactopyranose mutase / Actinobacterium-type cell wall biogenesis / UDP-galactopyranose mutase activity / capsule polysaccharide biosynthetic process / peptidoglycan-based cell wall / cell wall organization / flavin adenine dinucleotide binding / plasma membrane / 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 / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBeis, K. / 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. / Bamford, V.A. / Sanders, D.A. / 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.R. / Staines, A.G. / McMahon, S.A. / McNeil, M.R. / Whitfield, C. / Naismith, J.H.
History
DepositionMar 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _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 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 9, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other / Structure summary
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _struct.title
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-GALACTOPYRANOSE MUTASE
B: UDP-GALACTOPYRANOSE MUTASE
C: UDP-GALACTOPYRANOSE MUTASE
D: UDP-GALACTOPYRANOSE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,7789
Polymers183,4734
Non-polymers3,3055
Water18,3931021
1
A: UDP-GALACTOPYRANOSE MUTASE
C: UDP-GALACTOPYRANOSE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4715
Polymers91,7372
Non-polymers1,7343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-27 kcal/mol
Surface area33190 Å2
MethodPISA
2
B: UDP-GALACTOPYRANOSE MUTASE
D: UDP-GALACTOPYRANOSE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3084
Polymers91,7372
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-25 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.601, 153.733, 137.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2044-

HOH

21A-2316-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A4 - 137
2114B4 - 137
3114C4 - 137
4114D4 - 137
1214A142 - 395
2214B142 - 395
3214C142 - 395
4214D142 - 395
1126A1393
2126B1390
3126C1388
4126D1399 - 1388

NCS ensembles :
ID
1
2

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Components

#1: Protein
UDP-GALACTOPYRANOSE MUTASE / UDP-GALP MUTASE / NAD+-FLAVIN ADENINE DINUCLEOTIDE-REQUIRING ENZYME


Mass: 45868.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: FAD COFACTOR AND BICINE / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PET29B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O06934, UniProt: P9WIQ1*PLUS, UDP-galactopyranose mutase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 4 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M BICINE PH9.0, 1.6M AMMONIUM SULPHATE, 277K, pH 9.00

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.25→24.5 Å / Num. obs: 1188969 / % possible obs: 89 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.3
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.1 / % possible all: 85.2

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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: 2.25→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 6208 5.1 %RANDOM
Rwork0.225 ---
obs0.227 115830 88.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--0.48 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.25→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12648 0 223 1021 13892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213246
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.96218035
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5751544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99222.784704
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.997152012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.19915124
X-RAY DIFFRACTIONr_chiral_restr0.1090.21865
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210448
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.25963
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.28679
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2980
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4030.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7071.57941
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.162212448
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.77736247
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.774.55587
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3162medium positional0.270.5
12B3162medium positional0.250.5
13C3162medium positional0.230.5
14D3162medium positional0.230.5
21A53loose positional0.115
22B53loose positional0.15
23C53loose positional0.15
24D53loose positional0.145
11A3162medium thermal1.072
12B3162medium thermal0.982
13C3162medium thermal0.662
14D3162medium thermal0.692
21A53loose thermal1.6810
22B53loose thermal4.810
23C53loose thermal3.0210
24D53loose thermal3.1610
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 398 -
Rwork0.299 7917 -
obs--83.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67390.10590.050.2728-0.62661.57520.0637-0.03840.0275-0.0582-0.05560.02010.16340.2737-0.00810.0320.0735-0.0121-0.2014-0.0057-0.08922.7725.22727.164
24.80133.4837-7.04332.5821-5.795518.9672-0.25130.23280.383-0.09120.0703-0.2623-0.3919-0.50710.1810.00020.00020.00020.0011-0.00010.000143.00872.28835.354
32.1803-0.66350.29280.2105-0.12310.8792-0.1150.0380.30780.02880.0063-0.0519-0.2127-0.05390.10870.0117-0.0017-0.0353-0.21810.1050.0277-1.82833.3982.059
42.76320.8164-0.4120.2624-0.06330.9835-0.1942-0.0929-0.427-0.0740.0458-0.06140.2841-0.09040.14840.0509-0.03460.0347-0.10330.10790.02516.96543.71566.823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 395
2X-RAY DIFFRACTION1A1393
3X-RAY DIFFRACTION2B1 - 395
4X-RAY DIFFRACTION2B1390
5X-RAY DIFFRACTION3C1 - 395
6X-RAY DIFFRACTION3C1388
7X-RAY DIFFRACTION4D1 - 395
8X-RAY DIFFRACTION4D1388

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