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- PDB-1px0: Crystal structure of the haloalcohol dehalogenase HheC complexed ... -

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Basic information

Entry
Database: PDB / ID: 1px0
TitleCrystal structure of the haloalcohol dehalogenase HheC complexed with the haloalcohol mimic (R)-1-para-nitro-phenyl-2-azido-ethanol
Componentshalohydrin dehalogenase
KeywordsLYASE / HALOALCOHOL DEHALOGENASE / HALOHYDRIN DEHALOGENASE / HALOHYDRIN HYDROGEN-HALIDE LYASE / SDR FAMILY / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / ROSSMANN FOLD
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)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL / 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. / Rozeboom, H.J. / Kalk, K.H. / Tang, L. / Janssen, D.B. / Dijkstra, B.W.
CitationJournal: EMBO J. / Year: 2003
Title: Structure and Mechanism of a Bacterial Haloalcohol Dehalogenase: a new variation of the short-chain dehydrogenase/reductase fold without an NAD(P)H binding site
Authors: de Jong, R.M. / Tiesinga, J.J.W. / Rozeboom, H.J. / Kalk, K.H. / Tang, L. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionJul 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

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Assembly

Deposited unit
A: halohydrin dehalogenase
B: halohydrin dehalogenase
C: halohydrin dehalogenase
D: halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7518
Polymers111,9194
Non-polymers8334
Water16,250902
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19020 Å2
ΔGint-112 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.703, 71.843, 97.310
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the tetrameric biological assembly is generated by the two fold axis

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Components

#1: Protein
halohydrin dehalogenase


Mass: 27979.666 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: pGEF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93D82
#2: Chemical
ChemComp-RPN / (R)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL


Mass: 208.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H8N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: ammonium sulfate, bis-tris buffer, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
250 mM1reservoirNaBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 78669 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.049 / Net I/σ(I): 23.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 5.8 / Num. unique all: 7407 / Rsym value: 0.217 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 1029109
Reflection shell
*PLUS
Lowest resolution: 2 Å / % possible obs: 93.9 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PWX

1pwx


Resolution: 1.9→29.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2847900.29 / Data cutoff high rms absF: 2847900.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4547 5.8 %RANDOM
Rwork0.184 ---
obs0.184 78666 98.5 %-
all-83213 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.8007 Å2 / ksol: 0.385201 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å21.48 Å2
2---0.2 Å20 Å2
3----0.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.225 Å
Luzzati d res low-6 Å
Luzzati sigma a0.11 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7668 0 60 904 8632
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.42
X-RAY DIFFRACTIONc_scbond_it1.642
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 719 5.8 %
Rwork0.186 11747 -
obs-7407 94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5RNSAA2.PARAMRNSAA2.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97

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