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- PDB-7ang: MlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 7ang
TitleMlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni
ComponentsThymidine diphospho-4-keto-rhamnose 3,5-epimerase
KeywordsSUGAR BINDING PROTEIN / epimerise / sugar nucleotide / cupin fold / enzyme
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / polysaccharide biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsNaismith, J.H. / Woodward, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust100209/Z/12/Z) United Kingdom
CitationJournal: To Be Published
Title: MghlB
Authors: Naismith, J.H. / Woodward, L.
History
DepositionOct 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
B: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
C: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
D: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)82,9634
Polymers82,9634
Non-polymers00
Water1,20767
1
A: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
D: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)41,4812
Polymers41,4812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-9 kcal/mol
Surface area15820 Å2
MethodPISA
2
B: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
C: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)41,4812
Polymers41,4812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-8 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.258, 121.670, 153.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thymidine diphospho-4-keto-rhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D-xylo-4-hexulose 3


Mass: 20740.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: MghlB / Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: A0Z41_07375, A4277_09450, B4O43_09685, B7M65_03490, BGG25_09075, BM409_09635, BM444_09010, BM513_08715, BSK70_08235, BSO22_09160, BZL95_08990, C1418_09190, CLC11_09605, CUT57_09155, D6H09_ ...Gene: A0Z41_07375, A4277_09450, B4O43_09685, B7M65_03490, BGG25_09075, BM409_09635, BM444_09010, BM513_08715, BSK70_08235, BSO22_09160, BZL95_08990, C1418_09190, CLC11_09605, CUT57_09155, D6H09_04530, DDO06_09345, DDV78_09325, DMN69_08700, DNA92_09015, DUY83_08160, DYU98_09455, E7P31_08690, E7R39_08745, EID41_09365, F0020_07730, F0E95_08655, F0F84_08705, F0F98_08535, F0G47_08120, F0G48_09050, F0N28_08120, F1N65_08765, F1O83_08575, F6069_09535, F7J52_08685, F7N67_09750, F9736_08800, FJ686_08855, FLI41_08630, FLR61_08490, FM724_09165, FNQ00_09015, FNW64_09490, FQX08_09165, FR479_08460, FVI37_08595, FVM38_08185, FVM79_08160, FVN10_08670, FVY82_08610, FVZ89_08655, FW037_08340, FW114_08530, FW212_08130, FW254_07800, FW615_08225, FW631_08740, FW892_08160, FW922_08210, FWA46_08455, FWB30_08765, FWZ78_00520, FXA21_08555, FXA45_08490, FY829_09115, FZJ28_08750, FZV74_08235, GAU91_08625, GAX51_09520, GCY42_03565, GI147_08930, GI310_08945, GLM94_08700, GPY87_09225, GQ373_08515, GS576_08280, GSX00_06480, GTI33_08365, GTQ72_08215, GV351_09030, GWW43_07680, GXS63_001730, GZD67_001691, VQ12_003125
Production host: Escherichia coli (E. coli)
References: UniProt: A0A2U0QM91, UniProt: Q0P8I4*PLUS, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 31.05 % (w/v) PEG 1500, 0.25 M sodium-potassium phosphate, 3.83 % (v/v) 1,4-dioxane)

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.14→95.1 Å / Num. obs: 41762 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2944 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZR

1dzr


Resolution: 2.14→77.02 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 16.287 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23896 2202 5 %RANDOM
Rwork0.21469 ---
obs0.21594 41762 98.13 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.97 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.14→77.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 0 67 5704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195805
X-RAY DIFFRACTIONr_bond_other_d0.0010.025328
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.8757872
X-RAY DIFFRACTIONr_angle_other_deg1.0022.93912374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10424.043282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.236151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7331525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021240
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3662.5432710
X-RAY DIFFRACTIONr_mcbond_other2.3632.5422709
X-RAY DIFFRACTIONr_mcangle_it3.4963.8033377
X-RAY DIFFRACTIONr_mcangle_other3.4963.8053378
X-RAY DIFFRACTIONr_scbond_it2.9832.8983095
X-RAY DIFFRACTIONr_scbond_other2.9822.8993096
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5084.2144496
X-RAY DIFFRACTIONr_long_range_B_refined6.42729.0376321
X-RAY DIFFRACTIONr_long_range_B_other6.42628.9746310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 147 -
Rwork0.421 2944 -
obs--95.34 %
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)
12.3644-0.6749-0.33162.90431.15613.2750.0639-0.0143-0.14340.13340.0154-0.091-0.05130.1554-0.07930.0525-0.0227-0.02120.2511-0.09330.065739.19-23.0969.97
23.5557-0.7170.35092.8970.46845.9789-0.1973-0.30830.41850.3076-0.02660.4221-0.624-0.68090.22390.39850.03920.08350.3688-0.15020.368710.4179.8123.011
32.2749-1.0672-0.84924.2283-0.92436.65740.0440.20170.4052-0.2203-0.09530.1161-1.01480.27370.05130.4726-0.1173-0.05020.34570.03630.214522.32912.791-0.077
43.3334-0.80180.28032.07460.18234.5265-0.0034-0.4432-0.15030.40710.0153-0.2093-0.22240.3083-0.01180.3724-0.1146-0.06850.3687-0.02870.059640.879-15.39235.093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 180
2X-RAY DIFFRACTION2B4 - 178
3X-RAY DIFFRACTION3C5 - 175
4X-RAY DIFFRACTION4D5 - 180

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