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- PDB-5f3r: Structure of oxidized UDP-galactopyranose mutase from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 5f3r
TitleStructure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with magnesium ion
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / flavin adenine dinucleotide binding / metal ion 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 speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsWangkanont, K. / Kiessling, L.L. / Forest, K.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI063596 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100346 United States
CitationJournal: to be published
Title: Structural dynamics of UDP-galactopyranose mutase from Mycobacterium smegmatis
Authors: Wangkanont, K. / Kiessling, L.L. / Forest, K.T.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9085
Polymers47,9421
Non-polymers9664
Water3,567198
1
A: UDP-galactopyranose mutase
hetero molecules

A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,81710
Polymers95,8842
Non-polymers1,9328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4350 Å2
ΔGint-24 kcal/mol
Surface area34480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.989, 85.989, 126.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-502-

MG

21A-775-

HOH

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Components

#1: Protein UDP-galactopyranose mutase / UDP-galactopyranose mutase Glf


Mass: 47942.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: glf, MSMEG_6404, MSMEI_6236 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R629, 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM Tris-HCl, 25 mM MgCl2, 18% PEG 3350, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.04→42.2 Å / Num. obs: 30831 / % possible obs: 100 % / Redundancy: 28.4 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.014 / Rrim(I) all: 0.075 / Χ2: 0.849 / Net I/av σ(I): 47.138 / Net I/σ(I): 9.1 / Num. measured all: 874713
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.1227.40.92330240.9250.1760.940.63100
2.12-2.2127.70.61930090.9630.1180.630.653100
2.21-2.3128.10.44230350.9820.0840.450.667100
2.31-2.4328.50.330420.9920.0570.3050.689100
2.43-2.5828.80.20930230.9960.0390.2130.71100
2.58-2.7829.20.13630790.9980.0260.1390.733100
2.78-3.0629.30.08630640.9990.0160.0880.773100
3.06-3.529.10.07130900.9990.0130.0721.072100
3.5-4.4228.70.06931340.9990.0130.071.632100
4.42-42.226.90.04133310.9990.0080.0420.87699.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX(phenix.refine: 1.9_1690)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EQD

5eqd


Resolution: 2.04→40.696 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1498 4.98 %
Rwork0.1731 28558 -
obs0.1763 30056 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.27 Å2 / Biso mean: 52.1184 Å2 / Biso min: 29.21 Å2
Refinement stepCycle: final / Resolution: 2.04→40.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 62 198 3439
Biso mean--52.46 52.18 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073369
X-RAY DIFFRACTIONf_angle_d1.0634585
X-RAY DIFFRACTIONf_chiral_restr0.044471
X-RAY DIFFRACTIONf_plane_restr0.005601
X-RAY DIFFRACTIONf_dihedral_angle_d14.0881208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0397-2.10560.34491220.24662350247290
2.1056-2.18080.28211270.23382454258194
2.1808-2.26810.2881290.22422509263896
2.2681-2.37140.2811340.21032544267897
2.3714-2.49640.25811360.21432573270998
2.4964-2.65270.26141370.20592590272798
2.6527-2.85750.27971380.20382621275999
2.8575-3.1450.23921390.192826442783100
3.145-3.59980.22881420.179626982840100
3.5998-4.53450.20651420.139827142856100
4.5345-40.70390.22811520.146728613013100
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)
11.2238-0.10360.09161.7921-0.212.1518-0.1036-0.01080.2544-0.2365-0.01130.3171-0.3126-0.94970.04530.35280.0957-0.14190.5801-0.08240.4092-11.316624.083712.1636
21.60020.1262-0.89281.1809-0.17343.57340.0886-0.2548-0.1121-0.0105-0.1388-0.3122-0.15240.61960.060.3133-0.0708-0.02080.4557-0.00340.399114.83937.234228.5917
31.4825-0.0128-0.00382.7826-0.35882.6911-0.17530.07180.0847-0.49330.00230.10850.0014-0.51210.11720.2738-0.0218-0.10950.3697-0.09690.2718-4.234717.35498.7852
41.9536-1.1357-0.0321.87580.27922.4066-0.1588-0.09240.5654-0.2405-0.0846-0.2125-0.8464-0.1840.21870.52340.0215-0.17360.3288-0.07120.49593.126333.121410.4255
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 15:98)A15 - 98
2X-RAY DIFFRACTION2(chain A and resid 99:199)A99 - 199
3X-RAY DIFFRACTION3(chain A and resid 200:325)A200 - 325
4X-RAY DIFFRACTION4(chain A and resid 326:405)A326 - 405

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