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- PDB-4qed: ElxO Y152F with NADPH Bound -

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Basic information

Entry
Database: PDB / ID: 4qed
TitleElxO Y152F with NADPH Bound
ComponentsElxO
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


diacetyl reductase [(S)-acetoin forming] / monocarboxylic acid metabolic process / lipid metabolic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGarg, N. / Nair, S.K.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Substrate Specificity of the Lanthipeptide Peptidase ElxP and the Oxidoreductase ElxO.
Authors: Ortega, M.A. / Velasquez, J.E. / Garg, N. / Zhang, Q. / Joyce, R.E. / Nair, S.K. / van der Donk, W.A.
History
DepositionMay 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: ElxO
B: ElxO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5467
Polymers54,7712
Non-polymers1,7755
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-63 kcal/mol
Surface area21100 Å2
MethodPISA
2
A: ElxO
B: ElxO
hetero molecules

A: ElxO
B: ElxO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,09214
Polymers109,5424
Non-polymers3,55010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18630 Å2
ΔGint-173 kcal/mol
Surface area35170 Å2
MethodPISA
3
B: ElxO
hetero molecules

A: ElxO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5467
Polymers54,7712
Non-polymers1,7755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6230 Å2
ΔGint-63 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.424, 57.278, 82.438
Angle α, β, γ (deg.)90.00, 121.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ElxO


Mass: 27385.422 Da / Num. of mol.: 2 / Mutation: Y152F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: elxO / Production host: Escherichia coli (E. coli) / References: UniProt: I6ZQW6
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M ammonium acetate, 0.02 M magnesium chloride, 0.05 M HEPES-Na, 8% (v/v) PEG 800 5% (v/v) glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97624 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 42794 / Num. obs: 42794 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.054 / Net I/σ(I): 29.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 3481 / Rsym value: 0.268 / % possible all: 78.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.754 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20506 2168 5.1 %RANDOM
Rwork0.17896 ---
obs0.1803 40626 95.23 %-
all-40626 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.261 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å2-0 Å20.09 Å2
2--2.89 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 111 328 4279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9955436
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89225.625160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60215724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.922156
X-RAY DIFFRACTIONr_chiral_restr0.0790.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 105 -
Rwork0.227 2383 -
obs--75.49 %

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