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- PDB-1zo8: X-ray Structure of the haloalcohol dehalogenase HheC of Agrobacte... -

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Basic information

Entry
Database: PDB / ID: 1zo8
TitleX-ray Structure of the haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex with (S)-para-nitrostyrene oxide, with a water molecule in the halide-binding site
Componentshalohydrin dehalogenase
KeywordsLYASE / haloalcohol dehalogenase / halohydrin dehalogenase / enantioselectivity / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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
(S)-PARA-NITROSTYRENE OXIDE / 2,3-dichloro-1-propanol dehalogenase / Halohydrin dehalogenase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Authorsde Jong, R.M. / Tiesinga, J.J.W. / Tang, L. / Villa, A. / Janssen, D.B. / Dijkstra, B.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Structural Basis for the Enantioselectivity of an Epoxide Ring Opening Reaction Catalyzed by Halo Alcohol Dehalogenase HheC.
Authors: de Jong, R.M. / Tiesinga, J.J.W. / Villa, A. / Tang, L. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionMay 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: halohydrin dehalogenase
B: halohydrin dehalogenase
C: halohydrin dehalogenase
D: halohydrin dehalogenase
E: halohydrin dehalogenase
F: halohydrin dehalogenase
G: halohydrin dehalogenase
H: halohydrin dehalogenase
I: halohydrin dehalogenase
J: halohydrin dehalogenase
K: halohydrin dehalogenase
L: halohydrin dehalogenase
M: halohydrin dehalogenase
N: halohydrin dehalogenase
O: halohydrin dehalogenase
P: halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,31732
Polymers447,67516
Non-polymers2,64216
Water35,2011954
1
M: halohydrin dehalogenase
N: halohydrin dehalogenase
hetero molecules

M: halohydrin dehalogenase
N: halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5798
Polymers111,9194
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area18800 Å2
ΔGint-96 kcal/mol
Surface area30640 Å2
MethodPISA
2
A: halohydrin dehalogenase
B: halohydrin dehalogenase
C: halohydrin dehalogenase
D: halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5798
Polymers111,9194
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18710 Å2
ΔGint-96 kcal/mol
Surface area30650 Å2
MethodPISA
3
E: halohydrin dehalogenase
F: halohydrin dehalogenase
G: halohydrin dehalogenase
H: halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5798
Polymers111,9194
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18680 Å2
ΔGint-96 kcal/mol
Surface area30600 Å2
MethodPISA
4
O: halohydrin dehalogenase
P: halohydrin dehalogenase
hetero molecules

O: halohydrin dehalogenase
P: halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5798
Polymers111,9194
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area18720 Å2
ΔGint-95 kcal/mol
Surface area30390 Å2
MethodPISA
5
I: halohydrin dehalogenase
J: halohydrin dehalogenase
K: halohydrin dehalogenase
L: halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5798
Polymers111,9194
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18750 Å2
ΔGint-95 kcal/mol
Surface area30580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.753, 292.821, 146.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThere are three biologically relevant tetramers in the asymmetric unit, plus two dimers that form the relevant tetramers via the transformations 1_555, 2_655 and 1_555, 2_755

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Components

#1: Protein
halohydrin dehalogenase /


Mass: 27979.666 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: AD1 / Plasmid: pBADHheC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q7AUG5, UniProt: Q93D82*PLUS, EC: 4.5.-.-
#2: Chemical
ChemComp-SNO / (S)-PARA-NITROSTYRENE OXIDE / (2S)-2-(4-NITROPHENYL)OXIRANE


Mass: 165.146 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C8H7NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1954 / 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: 2.95 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 100 mM bis-Tris buffer, 50% ammoniumsulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2003 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 392451 / Num. obs: 392451 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.5 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 93.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zmt

1zmt


Resolution: 1.9→29.94 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5365299.66 / Data cutoff high rms absF: 5365299.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 20038 5.1 %RANDOM
Rwork0.208 ---
all0.216 412489 --
obs0.208 392451 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3125 Å2 / ksol: 0.387787 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---0.73 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30668 0 192 1954 32814
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.592
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 3173 5.1 %
Rwork0.233 59507 -
obs-37204 95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1&_1_PARAMETER_INFILE_1protein.top
X-RAY DIFFRACTION2pnso.pardna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5protein_rep.param

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