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- PDB-3sxp: Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-he... -

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Basic information

Entry
Database: PDB / ID: 3sxp
TitleCrystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD, HP0859)
ComponentsADP-L-glycero-D-mannoheptose-6-epimerase
KeywordsISOMERASE / Rossmann fold / Epimerase / NAD binding
Function / homology
Function and homology information


ADP-glyceromanno-heptose 6-epimerase activity / NADP binding / carbohydrate metabolic process
Similarity search - Function
ADP-L-glycero-D-manno-heptose-6-epimerase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / ADP-L-glycero-D-mannoheptose-6-epimerase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsShaik, M.M. / Zanotti, G. / Cendron, L.
Citation
Journal: Biochim.Biophys.Acta / Year: 2011
Title: The crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859) from Helicobacter pylori.
Authors: Shaik, M.M. / Zanotti, G. / Cendron, L.
#1: Journal: Structure / Year: 2000
Title: The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist
Authors: Deacon, A.M. / Ni, Y.S. / Coleman, W.G. / Ealick, S.E.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-L-glycero-D-mannoheptose-6-epimerase
B: ADP-L-glycero-D-mannoheptose-6-epimerase
C: ADP-L-glycero-D-mannoheptose-6-epimerase
D: ADP-L-glycero-D-mannoheptose-6-epimerase
E: ADP-L-glycero-D-mannoheptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,05610
Polymers205,7395
Non-polymers3,3175
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.940, 106.770, 152.220
Angle α, β, γ (deg.)90.00, 108.35, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
ADP-L-glycero-D-mannoheptose-6-epimerase


Mass: 41147.742 Da / Num. of mol.: 5 / Mutation: G7E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: hp0859, HPG27_813 / Plasmid: pET101-HP0859 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B5Z7L9, ADP-glyceromanno-heptose 6-epimerase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 0.2 M Ammonium Sulphate, 0.1M Tri Sodium citrate pH 5.6, 15% (w/v), PEG 4000, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→53.38 Å / Num. all: 55485 / Num. obs: 55485 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 4.8
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 1.8 / % possible all: 70.2

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Processing

Software
NameVersionClassification
CNS1.3refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EQ2

1eq2


Resolution: 2.55→53.39 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5954333.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2808 5.1 %RANDOM
Rwork0.239 ---
all0.241 55485 --
obs0.239 55485 85.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.1885 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å2-3.78 Å2
2--0.8 Å20 Å2
3---1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.55→53.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12448 0 220 245 12913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 373 4.9 %
Rwork0.356 7168 -
obs-6600 70.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6NAP.parNAP.top

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