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

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Basic information

Entry
Database: PDB / ID: 7ani
TitleDdahB, 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 / homologydTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Putative dTDP-4-dehydro rhamnose 3,5-epimerase
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: DdahB
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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0964
Polymers41,9122
Non-polymers1842
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-10 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.750, 68.190, 53.670
Angle α, β, γ (deg.)90.000, 91.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 5 - 175 / Label seq-ID: 5 - 175

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 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: 1.3→34.1 Å / Num. obs: 76397 / % possible obs: 95 % / Redundancy: 2.7 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4400 / CC1/2: 0.7 / % possible all: 75

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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: 1.3→34.1 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.589 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 4111 5.1 %RANDOM
Rwork0.1482 ---
obs0.1496 76397 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 72.36 Å2 / Biso mean: 22.351 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20.79 Å2
2---2.77 Å20 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 1.3→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 12 304 3157
Biso mean--33.49 35.93 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192966
X-RAY DIFFRACTIONr_bond_other_d0.0080.022833
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.944024
X-RAY DIFFRACTIONr_angle_other_deg1.34336530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86424.225142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74915516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7481512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213321
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02709
X-RAY DIFFRACTIONr_rigid_bond_restr2.60835799
X-RAY DIFFRACTIONr_sphericity_free33.842584
X-RAY DIFFRACTIONr_sphericity_bonded13.79955940
Refine LS restraints NCS

Ens-ID: 1 / Number: 19428 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 237 -
Rwork0.317 4400 -
all-4637 -
obs--74.5 %

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