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- PDB-6a41: Dehalogenation enzyme -

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Basic information

Entry
Database: PDB / ID: 6a41
TitleDehalogenation enzyme
Componentsdehalogenase
KeywordsOXIDOREDUCTASE / Dehalogenation
Function / homology: / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Dehalogenase
Function and homology information
Biological speciesRhodospirillaceae (purple nonsulfur bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsYin, B. / Yuan, A.Y.
CitationJournal: To Be Published
Title: Structure of a new dehalogenase at 1.9 Angstroms resolution
Authors: Yin, B. / Yuan, A.Y.
History
DepositionJun 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: dehalogenase


Theoretical massNumber of molelcules
Total (without water)26,2091
Polymers26,2091
Non-polymers00
Water3,297183
1
A: dehalogenase

A: dehalogenase

A: dehalogenase

A: dehalogenase


Theoretical massNumber of molelcules
Total (without water)104,8374
Polymers104,8374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area11840 Å2
ΔGint-81 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.895, 113.570, 141.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

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Components

#1: Protein dehalogenase


Mass: 26209.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillaceae (purple nonsulfur bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A5H1ZR29*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium Sulfate monohydrate, 0.1M Tris pH 8.5, 25% W/V Polyethylene Glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→70.96 Å / Num. obs: 18318 / % possible obs: 98.8 % / Redundancy: 6.3 % / Net I/σ(I): 50.6
Reflection shellResolution: 1.97→2.024 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→70.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.895 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18317 942 4.9 %RANDOM
Rwork0.14567 ---
obs0.14755 18318 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.122 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å2-0 Å2
2---1.36 Å2-0 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.97→70.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 0 183 2005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191861
X-RAY DIFFRACTIONr_bond_other_d0.0020.021775
X-RAY DIFFRACTIONr_angle_refined_deg2.2081.9782527
X-RAY DIFFRACTIONr_angle_other_deg1.1834096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16722.70374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69315275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4111515
X-RAY DIFFRACTIONr_chiral_restr0.1510.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212100
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02379
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.181975
X-RAY DIFFRACTIONr_mcbond_other1.1271.181974
X-RAY DIFFRACTIONr_mcangle_it1.7011.7621217
X-RAY DIFFRACTIONr_mcangle_other1.7011.7621218
X-RAY DIFFRACTIONr_scbond_it2.4081.551886
X-RAY DIFFRACTIONr_scbond_other2.4071.551887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.772.1741311
X-RAY DIFFRACTIONr_long_range_B_refined5.61715.9112115
X-RAY DIFFRACTIONr_long_range_B_other5.49615.6222081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.973→2.024 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 56 -
Rwork0.128 1289 -
obs--94.72 %
Refinement TLS params.Method: refined / Origin x: 2.9576 Å / Origin y: 15.9526 Å / Origin z: 14.7351 Å
111213212223313233
T0.0107 Å20.0003 Å20.0046 Å2-0.007 Å2-0.0044 Å2--0.0065 Å2
L0.213 °20.0066 °2-0.0142 °2-0.3352 °20.0606 °2--0.1646 °2
S0.0103 Å °0.0113 Å °0.0126 Å °0.0345 Å °0.018 Å °-0.009 Å °-0.0262 Å °0.0162 Å °-0.0283 Å °

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