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- PDB-5eqf: Crystal structure of oxidized UDP-galactopyranose mutase from Cor... -

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Basic information

Entry
Database: PDB / ID: 5eqf
TitleCrystal structure of oxidized UDP-galactopyranose mutase from Corynebacterium diphtheriae with UDP bound in closed form
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / galactofuranose
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / nucleotide binding
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 / URIDINE-5'-DIPHOSPHATE / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.145 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: Biochemistry / Year: 2017
Title: Conformational Control of UDP-Galactopyranose Mutase Inhibition.
Authors: Wangkanont, K. / Winton, V.J. / Forest, K.T. / Kiessling, L.L.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.5Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,17612
Polymers90,2202
Non-polymers2,95610
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-104 kcal/mol
Surface area31060 Å2
2
A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6847
Polymers45,1101
Non-polymers1,5746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4925
Polymers45,1101
Non-polymers1,3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.565, 82.691, 108.567
Angle α, β, γ (deg.)90.000, 112.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-403-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSchain AAA2 - 3875 - 390
2LEULEUchain BBB2 - 3865 - 389

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Components

#1: Protein UDP-galactopyranose mutase


Mass: 45109.973 Da / Num. of mol.: 2 / Fragment: residues 18-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: glf, DIP2203 / Plasmid: pMAL c5x
Details (production host): maltose binding protein in pMAL c5x was removed and replaced with His-tagged UDP-galactopyranose mutase
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NER4, UDP-galactopyranose mutase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris, 200 mM lithium sulfate, 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.145→30.4 Å / Num. obs: 50316 / % possible obs: 97.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 41.03 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.025 / Rrim(I) all: 0.069 / Χ2: 0.952 / Net I/av σ(I): 27.404 / Net I/σ(I): 10.6 / Num. measured all: 376968
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.145-2.235.80.41946370.9560.1810.4580.73990.5
2.23-2.327.20.37349490.9770.1470.4020.74296.8
2.32-2.427.80.2950010.9880.1110.3110.75297.6
2.42-2.557.80.22450780.990.0850.2390.79698
2.55-2.717.80.15150140.9950.0570.1610.85298.1
2.71-2.927.80.10950730.9970.0420.1170.94898.4
2.92-3.217.80.08150870.9980.0310.0871.09698.4
3.21-3.677.70.06450960.9980.0240.0691.25798.8
3.67-4.637.60.05551400.9980.0210.0591.33699
4.63-30.47.40.0452410.9990.0160.0430.90299.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å29.11 Å
Translation3 Å29.11 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata 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: 2.145→28.25 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 2382 4.99 %
Rwork0.1765 45316 -
obs0.179 47698 92.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.52 Å2 / Biso mean: 58.7074 Å2 / Biso min: 22.4 Å2
Refinement stepCycle: final / Resolution: 2.145→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 186 228 6736
Biso mean--64.25 50.24 -
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086714
X-RAY DIFFRACTIONf_angle_d1.1929137
X-RAY DIFFRACTIONf_chiral_restr0.051917
X-RAY DIFFRACTIONf_plane_restr0.0061184
X-RAY DIFFRACTIONf_dihedral_angle_d15.0642434
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3654X-RAY DIFFRACTION8.531TORSIONAL
12B3654X-RAY DIFFRACTION8.531TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1452-2.22180.30091890.24853546373572
2.2218-2.31070.26612080.22694109431784
2.3107-2.41590.26842260.20974330455689
2.4159-2.54320.27182390.21534501474092
2.5432-2.70240.27542440.21034618486295
2.7024-2.91080.23282530.20234732498596
2.9108-3.20340.27082520.21234791504397
3.2034-3.66610.25622550.18734827508298
3.6661-4.61560.21022580.14614891514999
4.6156-28.25260.17472580.1474971522999
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)
10.12780.0831-0.10450.0752-0.09520.0977-0.3756-0.07120.02250.02340.00240.0769-0.2605-0.5163-0.05310.92430.1716-0.27890.5108-0.12060.616653.313741.045817.2173
20.41360.20380.59380.8712-0.15210.8545-0.20010.16050.1164-0.1626-0.1773-0.0385-0.34580.0947-0.03190.48780.0475-0.03680.41680.00930.410368.22525.643819.6515
30.70730.01850.50040.4354-0.48070.7256-0.26860.0409-0.0188-0.15770.07720.0296-0.2228-0.0862-0.10340.42840.045-0.02160.27450.01780.213658.220824.530510.2111
40.1398-0.0407-0.05160.2379-0.16570.1766-0.53490.09810.23940.1178-0.1131-0.2428-0.60320.6356-0.0620.7712-0.1525-0.26760.57010.08220.620470.269143.551813.6757
50.72490.13670.17240.5577-0.19691.1924-0.0064-0.1332-0.0490.01080.0131-0.0392-0.05-0.178400.24580.08370.00970.2958-0.00160.323555.34981.51846.9232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 2:62)B2 - 62
2X-RAY DIFFRACTION2(chain B and resid 63:235)B63 - 235
3X-RAY DIFFRACTION3(chain B and resid 236:316)B236 - 316
4X-RAY DIFFRACTION4(chain B and resid 317:386)B317 - 386
5X-RAY DIFFRACTION5(chain A and resid 2:387)A2 - 387

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