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- PDB-6d99: Crystal structure of Corynebacterium diphtheriae UDP-galactopyran... -

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Basic information

Entry
Database: PDB / ID: 6d99
TitleCrystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-GalNAc (open, oxidized)
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / galatofuranose / galactopyranose / galactose / UDP / enzyme / UDP-galactopyranose mutase
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FLAVIN-ADENINE DINUCLEOTIDE / ISOPROPYL ALCOHOL / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / :
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsWangkanont, K. / Kiessling, L.L. / Forest, K.T.
Funding support United States, 3items
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 Allergy and Infectious Diseases (NIH/NIAID)R01 AI126592 United States
National Science Foundation (NSF, United States)IOS1353674 United States
CitationJournal: To be published
Title: Substrate recognition by FAD in UDP-galactopyranose mutase
Authors: Wangkanont, K. / Forest, K.T. / Kiessling, L.L.
History
DepositionApr 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4549
Polymers45,7381
Non-polymers1,7168
Water4,468248
1
A: UDP-galactopyranose mutase
hetero molecules

A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,90818
Polymers91,4752
Non-polymers3,43316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)98.010, 98.010, 127.280
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: UDP-galactopyranose mutase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: BU167_07490 / Plasmid: modified pMAL C5x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A246CDW5

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Non-polymers , 5 types, 256 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, 28% PEG400, 20% isopropanol

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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: Mar 13, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→46.87 Å / Num. obs: 64409 / % possible obs: 100 % / Redundancy: 29.1 % / Biso Wilson estimate: 36.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.029 / Rrim(I) all: 0.158 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.2229.40.88229270.9350.1650.898100
8.86-46.8722.90.0575800.9990.0120.05898.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.43 Å45.73 Å
Translation7.43 Å45.73 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BR7
Resolution: 2.15→45.732 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.21
RfactorNum. reflection% reflection
Rfree0.1871 1676 4.9 %
Rwork0.1532 --
obs0.1549 64409 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.18 Å2 / Biso mean: 39.4122 Å2 / Biso min: 19.84 Å2
Refinement stepCycle: final / Resolution: 2.15→45.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 113 248 3526
Biso mean--44.6 43.96 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083424
X-RAY DIFFRACTIONf_angle_d1.134660
X-RAY DIFFRACTIONf_chiral_restr0.047470
X-RAY DIFFRACTIONf_plane_restr0.005651
X-RAY DIFFRACTIONf_dihedral_angle_d13.9511293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.22690.25083240.201661316455
2.2269-2.3160.20133350.178960926427
2.316-2.42140.253450.170360926437
2.4214-2.54910.2113190.169961396458
2.5491-2.70880.21112960.163961446440
2.7088-2.91790.21493280.168860886416
2.9179-3.21140.20233070.169761526459
3.2114-3.6760.20932990.153861426441
3.676-4.63060.13653190.129961216440
4.6306-45.74270.16362840.137961526436

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