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

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Basic information

Entry
Database: PDB / ID: 1pwx
TitleCrystal structure of the haloalcohol dehalogenase HheC complexed with bromide
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
BROMIDE ION / Halohydrin dehalogenase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Feb 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,55812
Polymers111,9194
Non-polymers6398
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17840 Å2
ΔGint-126 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.213, 103.213, 117.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe asymmetric unit contains one biological functional tetramer

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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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.79 Å3/Da / Density % sol: 55.95 %
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: ELETTRA / Beamline: 5.2R / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 13, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.066 / Net I/σ(I): 23.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.05 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4234 / Rsym value: 0.164 / % possible all: 96.3
Reflection
*PLUS
Num. obs: 63725 / Num. measured all: 1561167 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 46.4 % / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
CNXACCELRYS INC. / CNS 1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Initial model from a low resolution MAD dataset, which has not been refined

Resolution: 1.8→38.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2198381.76 / Data cutoff high rms absF: 2198381.76 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: CRYSTAL IS A PERFECT TWIN: R/R FREE ARE TWINNED-R/R FREE
RfactorNum. reflection% reflectionSelection details
Rfree0.313 8691 7.8 %RANDOM
Rwork0.226 ---
all-119834 --
obs-111143 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.699 Å2 / ksol: 0.383578 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 1.8→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7668 0 8 525 8201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.12
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.413 1371 7.5 %
Rwork0.329 16863 -
obs-4234 96.8 %
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
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12

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