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- PDB-5br7: Structure of UDP-galactopyranose mutase from Corynebacterium diph... -

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Basic information

Entry
Database: PDB / ID: 5br7
TitleStructure of UDP-galactopyranose mutase from Corynebacterium diphtheriae in complex with citrate ion
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / UDP-galactopyranose mutase / Corynebacterium diphtheriae / galactofuranose / galactopyranose / citrate / FAD / sodium ion
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 / CITRATE ANION / ISOPROPYL ALCOHOL / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsWangkanont, K. / Kiessling, L.L. / Forest, K.T.
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
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,18712
Polymers45,7381
Non-polymers1,44911
Water8,251458
1
A: UDP-galactopyranose mutase
hetero molecules

A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,37424
Polymers91,4752
Non-polymers2,89822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-14 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.278, 98.278, 126.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-galactopyranose mutase /


Mass: 45737.668 Da / Num. of mol.: 1 / Fragment: UNP residues 18-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis) (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: glf, DIP2203 / Plasmid: pMAL c5x / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6NER4, UDP-galactopyranose mutase

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Non-polymers , 6 types, 469 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.3363.08
23.3363.08
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop5.6100 mM sodium citrate, 15% isopropanol, 16-18% PEG5000 MME
2982vapor diffusion, hanging drop5.6100 mM sodium citrate, 15% isopropanol, 16-18% PEG5000 MME. soaked in 100 mM potassium citrate, pH 5.6, 15% isopropanol, 18% PEG5000 MME prior to cryoprotection

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
SYNCHROTRONSSRL BL14-121.181
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 12, 2014
MARMOSAIC 325 mm CCD2CCDMay 21, 2015
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamond(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.1811
ReflectionResolution: 1.95→50 Å / Num. obs: 45492 / % possible obs: 99.9 % / Redundancy: 23.6 % / Biso Wilson estimate: 28.81 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.02 / Rrim(I) all: 0.105 / Χ2: 1.166 / Net I/av σ(I): 36.265 / Net I/σ(I): 8.7 / Num. measured all: 1075063
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.0220.10.75644540.9230.1640.7750.65599.6
2.02-2.120.70.52944670.9570.1130.5410.70599.6
2.1-2.221.20.37944570.9770.080.3880.73199.8
2.2-2.3121.70.27544840.9890.0580.2810.79799.9
2.31-2.4622.40.21345200.9930.0440.2170.88799.8
2.46-2.6523.30.16444980.9960.0340.1680.974100
2.65-2.9124.60.12545430.9980.0250.1271.13100
2.91-3.3326.30.10145760.9980.020.1031.527100
3.33-4.2280.09446180.9980.0180.0962.243100
4.2-5027.50.06248750.9990.0120.0631.40899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å46.72 Å
Translation3 Å46.72 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BI7

2bi7


Resolution: 1.95→46.72 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1895 2189 4.97 %
Rwork0.1528 41866 -
obs0.1546 44055 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.61 Å2 / Biso mean: 32.7926 Å2 / Biso min: 17.45 Å2
Refinement stepCycle: final / Resolution: 1.95→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 96 458 3719
Biso mean--34.31 41.2 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083508
X-RAY DIFFRACTIONf_angle_d1.0474761
X-RAY DIFFRACTIONf_chiral_restr0.044474
X-RAY DIFFRACTIONf_plane_restr0.004631
X-RAY DIFFRACTIONf_dihedral_angle_d14.631290
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 (%)
1.95-2.01970.22671910.19823616380785
2.0197-2.10050.22952020.18174003420593
2.1005-2.19610.21442140.17594038425295
2.1961-2.31190.20882130.17034129434296
2.3119-2.45670.21312220.16544190441297
2.4567-2.64640.21892190.16574240445998
2.6464-2.91270.20562250.17014304452999
2.9127-3.33410.22012280.162743334561100
3.3341-4.20010.16462310.137243944625100
4.2001-46.73350.15312440.128946194863100

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