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- PDB-4ej0: Crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase fr... -

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Basic information

Entry
Database: PDB / ID: 4ej0
TitleCrystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase from Burkholderia thailandensis
ComponentsADP-L-glycero-D-manno-heptose-6-epimerase
KeywordsISOMERASE / ADP-L-glycero-D-manno-heptose-6-epimerase / Modified Rossmann Fold / epimeration / NADP Binding / cytosol
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 / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / ADP-L-glycero-D-manno-heptose-6-epimerase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.609 Å
AuthorsKim, M.S. / Shin, D.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure and in silico substrate-binding mode of ADP-L-glycero-D-manno-heptose 6-epimerase from Burkholderia thailandensis.
Authors: Kim, M.S. / Lim, A. / Yang, S.W. / Park, J. / Lee, D. / Shin, D.H.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: ADP-L-glycero-D-manno-heptose-6-epimerase
B: ADP-L-glycero-D-manno-heptose-6-epimerase
C: ADP-L-glycero-D-manno-heptose-6-epimerase
D: ADP-L-glycero-D-manno-heptose-6-epimerase
E: ADP-L-glycero-D-manno-heptose-6-epimerase
F: ADP-L-glycero-D-manno-heptose-6-epimerase
G: ADP-L-glycero-D-manno-heptose-6-epimerase
H: ADP-L-glycero-D-manno-heptose-6-epimerase
I: ADP-L-glycero-D-manno-heptose-6-epimerase
J: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,96320
Polymers382,52910
Non-polymers7,43410
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
G: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
H: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
I: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
J: ADP-L-glycero-D-manno-heptose-6-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9962
Polymers38,2531
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.317, 160.923, 169.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ADP-L-glycero-D-manno-heptose-6-epimerase / ADP-L-glycero-beta-D-manno-heptose-6-epimerase / ADP-glyceromanno-heptose 6-epimerase / ADP-hep 6- ...ADP-L-glycero-beta-D-manno-heptose-6-epimerase / ADP-glyceromanno-heptose 6-epimerase / ADP-hep 6-epimerase / AGME


Mass: 38252.926 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: hldD, BTH_I1644 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2SY18, ADP-glyceromanno-heptose 6-epimerase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35% PEG 200, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2011
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.609→20.02 Å / Num. obs: 131360 / % possible obs: 83.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 5
Reflection shellHighest resolution: 2.61 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.609→19.971 Å / SU ML: 0.39 / σ(F): 1.4 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.241 6599 5.03 %Random
Rwork0.185 ---
all0.1878 131360 --
obs0.1878 131269 99.79 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.109 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0277 Å20 Å20 Å2
2--0.2309 Å2-0 Å2
3----0.2586 Å2
Refinement stepCycle: LAST / Resolution: 2.609→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26104 0 480 456 27040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00827194
X-RAY DIFFRACTIONf_angle_d1.13536808
X-RAY DIFFRACTIONf_dihedral_angle_d16.1579914
X-RAY DIFFRACTIONf_chiral_restr0.0723850
X-RAY DIFFRACTIONf_plane_restr0.0044844
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6094-2.6390.32212310.2508387694
2.639-2.670.30972340.24814048100
2.67-2.70250.33872170.24744123100
2.7025-2.73660.34772200.24944162100
2.7366-2.77250.32592150.24044125100
2.7725-2.81040.32642090.23724107100
2.8104-2.85040.30122260.22674127100
2.8504-2.89280.31752290.21454123100
2.8928-2.93790.3062590.21534116100
2.9379-2.98590.28542080.20714097100
2.9859-3.03720.27032250.19484161100
3.0372-3.09230.3012040.20534157100
3.0923-3.15150.29172460.20964096100
3.1515-3.21560.29992130.21044146100
3.2156-3.28520.26312300.20314123100
3.2852-3.36130.26432030.19694183100
3.3613-3.44490.23152120.19334135100
3.4449-3.53760.23382220.19674149100
3.5376-3.64110.23562100.18834158100
3.6411-3.75790.24221930.17344186100
3.7579-3.89120.24791930.17934205100
3.8912-4.04580.23562410.1784143100
4.0458-4.22830.21471950.15934208100
4.2283-4.44890.20282070.15434179100
4.4489-4.72410.19082230.15634208100
4.7241-5.08330.20412110.1554199100
5.0833-5.58470.20312300.16254209100
5.5847-6.36980.22482150.1924252100
6.3698-7.94040.21332400.17684268100
7.9404-19.97120.19382380.16594401100

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