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- PDB-4cf5: Mutagenesis of a Rhodobacteraceae L-haloacid dehalogenase -

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Basic information

Entry
Database: PDB / ID: 4cf5
TitleMutagenesis of a Rhodobacteraceae L-haloacid dehalogenase
ComponentsL-HALOACID DEHALOGENASE
KeywordsHYDROLASE
Function / homology
Function and homology information


(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity
Similarity search - Function
L-2-Haloacid dehalogenase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...L-2-Haloacid dehalogenase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase
Similarity search - Component
Biological speciesRHODOBACTERACEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsNovak, H.R. / Sayer, C. / Isupov, M.N. / Littlechild, J.A.
CitationJournal: To be Published
Title: Mutagenesis of a Rhodobacteraceae L-Haloacid Dehalogenase
Authors: Novak, H.R. / Sayer, C. / Isupov, M.N. / Littlechild, J.A.
History
DepositionNov 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-HALOACID DEHALOGENASE
B: L-HALOACID DEHALOGENASE
C: L-HALOACID DEHALOGENASE
D: L-HALOACID DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)103,2144
Polymers103,2144
Non-polymers00
Water4,360242
1
C: L-HALOACID DEHALOGENASE
D: L-HALOACID DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)51,6072
Polymers51,6072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-34.2 kcal/mol
Surface area17440 Å2
MethodPISA
2
A: L-HALOACID DEHALOGENASE
B: L-HALOACID DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)51,6072
Polymers51,6072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-32.4 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.320, 67.740, 284.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-HALOACID DEHALOGENASE


Mass: 25803.383 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTERACEAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL
References: UniProt: M9P6K0, UniProt: R4GRT2*PLUS, (S)-2-haloacid dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.02 Å3/Da / Density % sol: 39.15 % / Description: NONE
Crystal growpH: 8 / Details: pH 8

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.34→35.55 Å / Num. obs: 36556 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6
Reflection shellResolution: 2.34→2.4 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YML

2yml


Resolution: 2.34→35.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.684 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.272
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25028 1820 5 %RANDOM
Rwork0.17562 ---
obs0.17929 34659 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.34→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6948 0 0 242 7190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197129
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9769739
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72623.379290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.728151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0261546
X-RAY DIFFRACTIONr_chiral_restr0.0820.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0225450
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.988.8463600
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.54916.54493
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.049.1623529
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 140 -
Rwork0.256 2504 -
obs--99.77 %

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