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- PDB-6d2e: Crystal structure of Corynebacterium diphtheriae UDP-galactopyran... -

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Basic information

Entry
Database: PDB / ID: 6d2e
TitleCrystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-galactopyranose (open, oxidized)
ComponentsUDP-galactopyranose mutase
KeywordsISOMERASE / galatofuranose / galactopyranose / galactose / UDP / enzyme / UDP-galactopyranose mutase
Function / homology
Function and homology information


UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / flavin adenine dinucleotide 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 / GALACTOSE-URIDINE-5'-DIPHOSPHATE / ISOPROPYL ALCOHOL / : / UDP-galactopyranose mutase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 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

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Assembly

Deposited unit
A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4139
Polymers45,7381
Non-polymers1,6758
Water5,188288
1
A: UDP-galactopyranose mutase
hetero molecules

A: UDP-galactopyranose mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,82618
Polymers91,4752
Non-polymers3,35116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)98.410, 98.410, 127.820
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, UniProt: Q6NER4*PLUS

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Non-polymers , 5 types, 296 molecules

#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-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 288 / 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: 3.38 Å3/Da / Density % sol: 63.64 %
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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 3, 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: 2.05→33.572 Å / Num. obs: 75195 / % possible obs: 100 % / Redundancy: 29.3 % / Biso Wilson estimate: 36.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.019 / Rrim(I) all: 0.102 / Net I/σ(I): 22.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.1129.60.94933990.9210.1770.965100
8.45-33.5723.40.0486680.9990.010.04998.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.45 Å33.57 Å
Translation7.45 Å33.57 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BR7

5br7


Resolution: 2.05→33.572 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.17
RfactorNum. reflection% reflection
Rfree0.1956 1974 4.92 %
Rwork0.1612 --
obs0.1629 75195 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.52 Å2 / Biso mean: 40.1558 Å2 / Biso min: 23.65 Å2
Refinement stepCycle: final / Resolution: 2.05→33.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 110 288 3563
Biso mean--42.01 44.64 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083371
X-RAY DIFFRACTIONf_angle_d1.0914582
X-RAY DIFFRACTIONf_chiral_restr0.046464
X-RAY DIFFRACTIONf_plane_restr0.004638
X-RAY DIFFRACTIONf_dihedral_angle_d13.2521267
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
2.05-2.12330.27183330.229871787511
2.1233-2.20830.23813750.204671347509
2.2083-2.30880.20124000.183171227522
2.3088-2.43050.22763930.173171237516
2.4305-2.58270.20653400.172671897529
2.5827-2.7820.21013270.174171997526
2.782-3.06180.21693680.18371607528
3.0618-3.50440.19854010.171871287529
3.5044-4.41360.16623780.142671147492
4.4136-33.57610.18193840.134271497533

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