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- PDB-1zmo: Apo structure of haloalcohol dehalogenase HheA of Arthrobacter sp. AD2 -

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Basic information

Entry
Database: PDB / ID: 1zmo
TitleApo structure of haloalcohol dehalogenase HheA of Arthrobacter sp. AD2
Componentshalohydrin dehalogenase
KeywordsLYASE / halohydrin dehalogenase / haloalcohol dehalogenase / short-chain dehydrogenase/reductase family
Function / homologyEnoyl-(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 / Halohydrin dehalogenase
Function and homology information
Biological speciesArthrobacter sp. AD2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsde Jong, R.M. / Kalk, K.H. / Tang, L. / Janssen, D.B. / Dijkstra, B.W.
CitationJournal: J.Bacteriol. / Year: 2006
Title: The X-ray structure of the haloalcohol dehalogenase HheA from Arthrobacter sp. strain AD2: insight into enantioselectivity and halide binding in the haloalcohol dehalogenase family.
Authors: de Jong, R.M. / Kalk, K.H. / Tang, L. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: halohydrin dehalogenase
F: halohydrin dehalogenase
G: halohydrin dehalogenase
H: halohydrin dehalogenase


Theoretical massNumber of molelcules
Total (without water)211,6088
Polymers211,6088
Non-polymers00
Water15,529862
1
E: halohydrin dehalogenase
F: halohydrin dehalogenase
G: halohydrin dehalogenase
H: halohydrin dehalogenase


Theoretical massNumber of molelcules
Total (without water)105,8044
Polymers105,8044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-75 kcal/mol
Surface area31690 Å2
MethodPISA
2
A: halohydrin dehalogenase
B: halohydrin dehalogenase
C: halohydrin dehalogenase
D: halohydrin dehalogenase


Theoretical massNumber of molelcules
Total (without water)105,8044
Polymers105,8044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-72 kcal/mol
Surface area31650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.980, 77.720, 111.422
Angle α, β, γ (deg.)97.29, 89.97, 112.98
Int Tables number1
Space group name H-MP1
DetailsThere are two biologically active tetramers in the asymmetric unit.

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Components

#1: Protein
halohydrin dehalogenase


Mass: 26451.004 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. AD2 (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93MS3, EC: 4.5.-.-
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.52 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% w/v PEG 8000, 100 mM MES buffer, 100 mM Magnesium Acetate, 50 mM Sodium Formate, pH 6.5, 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: 2→25 Å / Num. obs: 120343 / % possible obs: 89.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 10.2 Å2
Reflection shellResolution: 2→2.09 Å / % possible all: 89.4

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Processing

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

1pwx


Resolution: 2→20.05 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1374501.74 / Data cutoff high rms absF: 1374501.74 / 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
Rfree0.273 6020 5 %RANDOM
Rwork0.218 ---
all0.223 126036 --
obs0.218 120016 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.2387 Å2 / ksol: 0.416166 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å24.6 Å20.39 Å2
2--5.29 Å20.52 Å2
3----4.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→20.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14554 0 0 862 15416
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.47
X-RAY DIFFRACTIONc_mcbond_it2.191.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it3.382
X-RAY DIFFRACTIONc_scangle_it4.142.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 921 5.1 %
Rwork0.253 17275 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1&_1_PARAMETER_INFILE_1protein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5protein_rep.param

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