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- PDB-7an4: MlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni ... -

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Basic information

Entry
Database: PDB / ID: 7an4
TitleMlghB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni complex with GDP-mannose
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 / dTDP-rhamnose biosynthetic process / extracellular 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
GUANOSINE-5'-DIPHOSPHATE / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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 with GDP
Authors: Naismith, J.H. / Woodward, L.
History
DepositionOct 10, 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 / 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7468
Polymers84,9734
Non-polymers1,7734
Water1448
1
A: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
B: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3734
Polymers42,4862
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-21 kcal/mol
Surface area15570 Å2
MethodPISA
2
D: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
hetero molecules

C: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)43,3734
Polymers42,4862
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4920 Å2
ΔGint-23 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.350, 121.880, 154.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA2 - 1764 - 178
21ALAALABB2 - 1764 - 178
12METMETAA1 - 1763 - 178
22METMETCC1 - 1763 - 178
13ALAALAAA2 - 1764 - 178
23ALAALADD2 - 1764 - 178
14ALAALABB2 - 1764 - 178
24ALAALACC2 - 1764 - 178
15ALAALABB2 - 1764 - 178
25ALAALADD2 - 1764 - 178
16ALAALACC2 - 1764 - 178
26ALAALADD2 - 1764 - 178

NCS ensembles :
ID
1
2
3
4
5
6

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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: 21243.232 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.42 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→56.7 Å / Num. obs: 23972 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.162 / Net I/σ(I): 12.5
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1611 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZR

1dzr


Resolution: 2.6→56.67 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.901 / SU B: 11.204 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.581 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1263 5 %RANDOM
Rwork0.2108 ---
obs0.212 23972 99.34 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.81 Å2 / Biso mean: 26.456 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--1.78 Å20 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 2.6→56.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5858 0 112 8 5978
Biso mean--47.15 15.63 -
Num. residues----708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196142
X-RAY DIFFRACTIONr_bond_other_d0.0060.025684
X-RAY DIFFRACTIONr_angle_refined_deg1.571.978362
X-RAY DIFFRACTIONr_angle_other_deg1.326313116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2524.247292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.959151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7541524
X-RAY DIFFRACTIONr_chiral_restr0.0890.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216752
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021440
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A208040.1
12B208040.1
21A215980.08
22C215980.08
31A213760.08
32D213760.08
41B211200.09
42C211200.09
51B213280.08
52D213280.08
61C216680.07
62D216680.07
LS refinement shellResolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 90 -
Rwork0.294 1613 -
all-1703 -
obs--91.66 %

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