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- PDB-2ymm: Sulfate bound L-haloacid dehalogenase from a Rhodobacteraceae fam... -

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Basic information

Entry
Database: PDB / ID: 2ymm
TitleSulfate bound L-haloacid dehalogenase from a Rhodobacteraceae family bacterium
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
Similarity search - Component
Biological speciesRHODOBACTERACEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsNovak, H.R. / Sayer, C. / Isupov, M.N. / Paszkiewicz, K. / Gotz, D. / Spragg, A.M. / Littlechild, J.A.
CitationJournal: FEBS J. / Year: 2013
Title: Marine Rhodobacteraceae L-Haloacid Dehalogenase Contains a Novel His/Glu Dyad that Could Activate the Catalytic Water.
Authors: Novak, H.R. / Sayer, C. / Isupov, M.N. / Paszkiewicz, K. / Gotz, D. / Mearns Spragg, A. / Littlechild, J.A.
History
DepositionOct 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Atomic model
Revision 1.2Dec 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_site
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_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
A: L-HALOACID DEHALOGENASE
B: L-HALOACID DEHALOGENASE
C: L-HALOACID DEHALOGENASE
D: L-HALOACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3708
Polymers102,9854
Non-polymers3844
Water14,628812
1
C: L-HALOACID DEHALOGENASE
D: L-HALOACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6854
Polymers51,4932
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-75.2 kcal/mol
Surface area17470 Å2
MethodPISA
2
A: L-HALOACID DEHALOGENASE
B: L-HALOACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6854
Polymers51,4932
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-74.6 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.780, 68.550, 283.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99993, 0.01095, 0.00383), (0.00529, 0.72422, -0.68955), (-0.01032, -0.68948, -0.72423)-19.12816, -57.95612, -145.3053
2given(-0.99993, 0.01095, 0.00383), (0.00529, 0.72422, -0.68955), (-0.01032, -0.68948, -0.72423)-19.12816, -57.95612, -145.3053
3given(-0.99883, 0.00663, -0.04797), (0.03005, -0.69197, -0.7213), (-0.03798, -0.7219, 0.69096)-6.09838, -66.372, 71.88003

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Components

#1: Protein
L-HALOACID DEHALOGENASE


Mass: 25746.334 Da / Num. of mol.: 4
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): RIPL / References: UniProt: R4GRT2*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE MATCHES TO GENBANK JX868516

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 37.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.64→55.34 Å / Num. obs: 97923 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 1.64→1.68 Å / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YML

2yml


Resolution: 1.64→55.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.876 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20502 5153 5 %RANDOM
Rwork0.16301 ---
obs0.1651 97923 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.791 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.64→55.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6940 0 20 812 7772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197899
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.98210981
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17851135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61824.012344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.115151321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0451553
X-RAY DIFFRACTIONr_chiral_restr0.0920.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216181
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.642→1.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 393 -
Rwork0.272 7086 -
obs--99.67 %

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