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- PDB-1zmt: Structure of haloalcohol dehalogenase HheC of Agrobacterium radio... -

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Basic information

Entry
Database: PDB / ID: 1zmt
TitleStructure of haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex with (R)-para-nitro styrene oxide, with a water molecule in the halide-binding site
ComponentsHaloalcohol dehalogenase HheC
KeywordsLYASE / haloalcohol dehalogenase / halohydrin dehalogenase / epoxide catalysis / enantioselectivity
Function / homology
Function and homology information


: / 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
(R)-PARA-NITROSTYRENE OXIDE / Halohydrin dehalogenase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Authorsde Jong, R.M. / Tiesinga, J.J.W. / Villa, A. / Tang, L. / 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 10, 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Haloalcohol dehalogenase HheC
B: Haloalcohol dehalogenase HheC
C: Haloalcohol dehalogenase HheC
D: Haloalcohol dehalogenase HheC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5798
Polymers111,9194
Non-polymers6614
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18660 Å2
ΔGint-92 kcal/mol
Surface area30690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.444, 72.041, 97.420
Angle α, β, γ (deg.)90.00, 92.88, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains two dimers that form two biologically relevant tetramers

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Components

#1: Protein
Haloalcohol dehalogenase HheC


Mass: 27979.666 Da / Num. of mol.: 4
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: Q93D82
#2: Chemical
ChemComp-RNO / (R)-PARA-NITROSTYRENE OXIDE / (2R)-2-(4-NITROPHENYL)OXIRANE


Mass: 165.146 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.37 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM bis-Tris buffer, 50% Ammonium sulfate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2003
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 112897 / Num. obs: 110598 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.9 Å2
Reflection shellResolution: 1.7→1.81 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27.2 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2431700.55 / Data cutoff high rms absF: 2431700.55 / 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
Rfree0.224 8023 7.3 %RANDOM
Rwork0.199 ---
all0.202 ---
obs0.199 110598 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.6245 Å2 / ksol: 0.425254 e/Å3
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20.12 Å2
2--0.48 Å20 Å2
3----2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 0 48 716 8436
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_d0.92
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.372
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 1338 7.5 %
Rwork0.266 16534 -
obs--96.7 %
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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