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

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Basic information

Entry
Database: PDB / ID: 1pwz
TitleCrystal structure of the haloalcohol dehalogenase HheC complexed with (R)-styrene oxide and chloride
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-STYRENE OXIDE / Halohydrin dehalogenase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Derived calculations / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,2716
Polymers55,9592
Non-polymers3114
Water1,15364
1
A: halohydrin dehalogenase
B: halohydrin dehalogenase
hetero molecules

A: halohydrin dehalogenase
B: halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,54112
Polymers111,9194
Non-polymers6228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area18890 Å2
ΔGint-162 kcal/mol
Surface area30620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.904, 103.904, 119.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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.: 2
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-RSO / R-STYRENE OXIDE


Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
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: ID14-2 / Wavelength: 1.01 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.5→37 Å / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.096 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.41 / % possible all: 91.7
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Num. obs: 20596 / % possible obs: 96.3 % / Num. measured all: 197117 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / % possible obs: 91.7 % / Rmerge(I) obs: 0.41

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PWX

1pwx


Resolution: 2.5→37.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2179208.25 / 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
Rfree0.271 1172 5.2 %RANDOM
Rwork0.224 ---
obs0.224 22581 97.1 %-
all-23753 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.7236 Å2 / ksol: 0.354233 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2---1.94 Å20 Å2
3---3.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 20 64 3914
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 205 5.4 %
Rwork0.314 3580 -
obs--99.7 %
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 DIFFRACTION5RSO.PARAMRSO.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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