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- PDB-3afi: Crystal structure of DBJA (HIS-DBJA) -

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Basic information

Entry
Database: PDB / ID: 3afi
TitleCrystal structure of DBJA (HIS-DBJA)
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / A/B-HYDROLASE
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / hydrolase activity / identical protein binding
Similarity search - Function
: / Haloalkane dehalogenase, subfamily 2 / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Haloalkane dehalogenase
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSato, Y. / Senda, T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Authors: Prokop, Z. / Sato, Y. / Brezovsky, J. / Mozga, T. / Chaloupkova, R. / Koudelakova, T. / Jerabek, P. / Stepankova, V. / Natsume, R. / van Leeuwen, J.G. / Janssen, D.B. / Florian, J. / Nagata, ...Authors: Prokop, Z. / Sato, Y. / Brezovsky, J. / Mozga, T. / Chaloupkova, R. / Koudelakova, T. / Jerabek, P. / Stepankova, V. / Natsume, R. / van Leeuwen, J.G. / Janssen, D.B. / Florian, J. / Nagata, Y. / Senda, T. / Damborsky, J.
History
DepositionMar 2, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
E: Haloalkane dehalogenase
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
F: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,9778
Polymers139,8354
Non-polymers1424
Water20,1771120
1
E: Haloalkane dehalogenase
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9884
Polymers69,9182
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-9 kcal/mol
Surface area23580 Å2
MethodPISA
2
B: Haloalkane dehalogenase
F: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9884
Polymers69,9182
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-9 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.855, 117.843, 55.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Haloalkane dehalogenase


Mass: 34958.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: DBJA / Plasmid: PYBJA2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59337, haloalkane dehalogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1120 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: PEG 4000, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2005
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 134673 / % possible obs: 95.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.041
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.175 / % possible all: 90.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0005refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BN6

1bn6


Resolution: 1.75→35.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.819 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19076 6770 5 %RANDOM
Rwork0.16674 ---
obs0.16794 127902 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9401 0 4 1120 10525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229701
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.94713209
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18451196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60521.875464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.553151424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.02815100
X-RAY DIFFRACTIONr_chiral_restr0.0890.21405
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217690
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.24700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.26684
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2963
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6541.56028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23329656
X-RAY DIFFRACTIONr_scbond_it233673
X-RAY DIFFRACTIONr_scangle_it3.3664.53553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.753→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 450 -
Rwork0.184 8607 -
obs--87.86 %

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