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- PDB-1eq2: THE CRYSTAL STRUCTURE OF ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE -

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Basic information

Entry
Database: PDB / ID: 1eq2
TitleTHE CRYSTAL STRUCTURE OF ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
ComponentsADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
KeywordsISOMERASE / N-terminal domain Rossmann fold / C-terminal mixed alpha/beta domain / Short-chain dehydrogenase/reductase fold
Function / homology
Function and homology information


ADP-glyceromanno-heptose 6-epimerase / ADP-glyceromanno-heptose 6-epimerase activity / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / NADP+ binding / membrane / cytosol
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
ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / ADP-L-glycero-D-manno-heptose-6-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsDeacon, A.M. / Ni, Y.S. / Coleman Jr., W.G. / Ealick, S.E.
Citation
Journal: Structure Fold.Des. / 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 Jr., W.G. / Ealick, S.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Diffraction Studies of the Lipopolysaccharide Core Biosynthetic Enzyme ADP-L-glycero-D-mannoheptose 6-epimerase from Escherichia coli K-12
Authors: Ding, L. / Zhang, Y. / Deacon, A.M. / Ealick, S.E. / Ni, Y. / Sun, P. / Coleman Jr., W.G.
History
DepositionMar 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / struct_conn / 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 / _entity.details / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
F: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
G: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
H: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
I: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
J: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,75830
Polymers349,43010
Non-polymers13,32720
Water19,0241056
1
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)181,37915
Polymers174,7155
Non-polymers6,66410
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
G: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
H: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
I: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
J: ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,37915
Polymers174,7155
Non-polymers6,66410
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.46, 109.76, 181.54
Angle α, β, γ (deg.)90, 91.04, 90
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a pentamer. There are two pentamers in the asymmetric unit, each with a local non-crystallographic five-fold axis parallel to the crystallographic two-fold screw axis.

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Components

#1: Protein
ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE


Mass: 34943.031 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7-5 / Production host: Escherichia coli (E. coli)
References: UniProt: P67910, ADP-glyceromanno-heptose 6-epimerase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Details: Sigma
#3: Chemical
ChemComp-ADQ / ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / ADENOSINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 589.342 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H25N5O15P2 / Details: Sigma
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1056 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M ammonium sulphate, 2% PEG400, 0.1M HEPES buffer, 1mM ADP-glucose, 20nM spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
32 %PEG4001reservoir
40.1 MHEPES1reservoirpH7.5
51 mMADP-glucose1reservoir
61 mM1reservoirNaN3
720 mMspermidine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.919
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 242386 / Num. obs: 242386 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.218 / Num. unique all: 239829 / % possible all: 78.6
Reflection
*PLUS
Num. measured all: 573756
Reflection shell
*PLUS
% possible obs: 78.6 % / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
SnBphasing
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→20 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 24373 -10% of reflections chosen at random
Rwork0.212 ---
all0.217 242238 --
obs0.217 242238 93.3 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23596 0 783 1056 25435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.5
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.5

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