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- PDB-8do5: Crystal structure of NahE in complex with intermediate (R)-4-hydr... -

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Basic information

Entry
Database: PDB / ID: 8do5
TitleCrystal structure of NahE in complex with intermediate (R)-4-hydroxy-4-(2-hydroxyphenyl)-2-iminobutanoate
ComponentsTrans-ohydrobenzylidenepyruvate hydratase aldolase
KeywordsLYASE / hydratase-aldolase / TIM / hydratase / aldolase
Function / homologyDapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel / lyase activity / (4R)-4-hydroxy-4-(2-hydroxyphenyl)butanoic acid / Trans-ohydrobenzylidenepyruvate hydratase aldolase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLeVieux, J.A. / Hardtke, H.A. / Zhang, Y.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)41239 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)104896 United States
Robert A. Welch Foundation1334 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2023
Title: A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway.
Authors: Lancaster, E.B. / Johnson Jr., W.H. / LeVieux, J.A. / Hardtke, H.A. / Zhang, Y.J. / Whitman, C.P.
History
DepositionJul 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trans-ohydrobenzylidenepyruvate hydratase aldolase
B: Trans-ohydrobenzylidenepyruvate hydratase aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9036
Polymers73,3542
Non-polymers5494
Water3,243180
1
A: Trans-ohydrobenzylidenepyruvate hydratase aldolase
B: Trans-ohydrobenzylidenepyruvate hydratase aldolase
hetero molecules

A: Trans-ohydrobenzylidenepyruvate hydratase aldolase
B: Trans-ohydrobenzylidenepyruvate hydratase aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,80512
Polymers146,7084
Non-polymers1,0978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)87.999, 87.999, 141.599
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Trans-ohydrobenzylidenepyruvate hydratase aldolase


Mass: 36676.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: nahE / Production host: Escherichia coli (E. coli) / References: UniProt: Q0KK75
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-KRN / (4R)-4-hydroxy-4-(2-hydroxyphenyl)butanoic acid


Mass: 196.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 23% PEG 2000 MME, 0.1 M MES (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→44 Å / Num. obs: 37736 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 28.41 Å2 / CC1/2: 0.886 / Rpim(I) all: 0.042 / Rsym value: 0.129 / Net I/σ(I): 20.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2004 / Rpim(I) all: 0.269 / Rsym value: 0.854 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SVT5

Resolution: 2.1→44 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 2004 5.36 %
Rwork0.2021 35391 -
obs0.2054 37395 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 36 180 5238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735180
X-RAY DIFFRACTIONf_angle_d0.86727047
X-RAY DIFFRACTIONf_chiral_restr0.0514773
X-RAY DIFFRACTIONf_plane_restr0.0081910
X-RAY DIFFRACTIONf_dihedral_angle_d7.8568716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.3251400.23922478X-RAY DIFFRACTION98.9
2.15-2.210.32181410.23152487X-RAY DIFFRACTION99.28
2.21-2.280.5051370.39662349X-RAY DIFFRACTION94.35
2.28-2.350.29481470.2332530X-RAY DIFFRACTION99.41
2.35-2.430.26761410.23342491X-RAY DIFFRACTION99.43
2.43-2.530.26741400.22342510X-RAY DIFFRACTION99.33
2.53-2.650.29161420.24472517X-RAY DIFFRACTION99.85
2.65-2.780.31461440.24672514X-RAY DIFFRACTION99.66
2.79-2.960.33571430.23692528X-RAY DIFFRACTION99.74
2.96-3.190.30251410.21362558X-RAY DIFFRACTION99.85
3.19-3.510.29891440.20832528X-RAY DIFFRACTION99.7
3.51-4.020.22521460.18062585X-RAY DIFFRACTION99.67
4.02-5.060.18771440.14542594X-RAY DIFFRACTION99.85
5.06-440.18961540.14922722X-RAY DIFFRACTION99.97

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