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- PDB-7anj: DdahB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni ... -

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Basic information

Entry
Database: PDB / ID: 7anj
TitleDdahB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni complexed to 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 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-ALPHA-D-MANNOSE / GUANOSINE-5'-DIPHOSPHATE / Putative dTDP-4-dehydro rhamnose 3,5-epimerase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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: DdhaB with GDP-mannose
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9604
Polymers41,9122
Non-polymers1,0492
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-13 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.001, 67.810, 53.140
Angle α, β, γ (deg.)90.000, 91.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 176
2010B4 - 176

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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: 20955.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: BBR99_05345, D0W34_08620, D5I02_08520, F0H18_08555, F1P94_09915, FRS42_06315, FVZ69_07850, FW031_08545, FW918_03925, FWZ96_07945, GAX04_08395, GJ442_08190, GRS20_08795, GSH24_04195, GY415_ ...Gene: BBR99_05345, D0W34_08620, D5I02_08520, F0H18_08555, F1P94_09915, FRS42_06315, FVZ69_07850, FW031_08545, FW918_03925, FWZ96_07945, GAX04_08395, GJ442_08190, GRS20_08795, GSH24_04195, GY415_001377, GZD82_001464, HS23.15
Production host: Escherichia coli (E. coli)
References: UniProt: Q6EF58, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 24 % (w/v) PEG 1500, 20 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→53.11 Å / Num. obs: 13466 / % possible obs: 98 % / Redundancy: 3.6 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 879 / CC1/2: 0.9 / % possible all: 89

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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: 2.35→53.11 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.741 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.525 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 675 4.8 %RANDOM
Rwork0.1852 ---
obs0.188 13466 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.13 Å2 / Biso mean: 21.312 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.65 Å2
2---0.53 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.35→53.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 67 46 2855
Biso mean--45.5 11.14 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192884
X-RAY DIFFRACTIONr_bond_other_d0.0030.022698
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9643921
X-RAY DIFFRACTIONr_angle_other_deg0.96836206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9435330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22524135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81215481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8691512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023160
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02692
Refine LS restraints NCS

Ens-ID: 1 / Number: 19512 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.35→2.407 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.315 46 -
Rwork0.194 879 -
obs--86.77 %

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