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- PDB-3umg: Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase... -

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Basic information

Entry
Database: PDB / ID: 3umg
TitleCrystal Structure of the Defluorinating L-2-Haloacid Dehalogenase Rha0230
ComponentsHaloacid dehalogenase
KeywordsHYDROLASE / Haloacid dehalogenase-like hydrolase protein superfamily / defluorinase
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 / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...L-2-Haloacid dehalogenase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / 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
Haloacid dehalogenase
Similarity search - Component
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChan, P.W.Y. / Savchenko, A. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F.
CitationJournal: To be Published
Title: Structural adaptations of L-2-haloacid dehalogenases that enable hydrolytic defluorination
Authors: Chan, P.W.Y. / To, T.K.W. / Petit, P. / Tran, C. / Waelti, M. / Savchenko, A. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F.
History
DepositionNov 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Haloacid dehalogenase
B: Haloacid dehalogenase
C: Haloacid dehalogenase
D: Haloacid dehalogenase
E: Haloacid dehalogenase
F: Haloacid dehalogenase
G: Haloacid dehalogenase
H: Haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,69515
Polymers220,4478
Non-polymers2487
Water8,323462
1
A: Haloacid dehalogenase
B: Haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1473
Polymers55,1122
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-19 kcal/mol
Surface area19930 Å2
MethodPISA
2
C: Haloacid dehalogenase
D: Haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1834
Polymers55,1122
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-30 kcal/mol
Surface area19970 Å2
MethodPISA
3
E: Haloacid dehalogenase
F: Haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1834
Polymers55,1122
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-31 kcal/mol
Surface area20060 Å2
MethodPISA
4
G: Haloacid dehalogenase
H: Haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1834
Polymers55,1122
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-31 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.180, 148.650, 152.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 254
2116B1 - 254
3116C1 - 254
4116D1 - 254
5116E1 - 254
6116F1 - 254
7116G1 - 254
8116H1 - 254

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Components

#1: Protein
Haloacid dehalogenase / L-2-Haloacid Dehalogenase Rha0230


Mass: 27555.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Gene: RHA1_ro00230 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0SK70, (S)-2-haloacid dehalogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6 M trisodium citrate, 0.1 M sodium HEPES, pH 7.5, cryoprotectant: reservoir solution + 16% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2006
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→38.491 Å / Num. obs: 107063 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.478 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.25-2.310.4683.8839227791298
2.31-2.370.3554.7238779776998.4
2.37-2.440.3295.0237859757198.2
2.44-2.520.276.1536604731998.2
2.52-2.60.2287.1935553710298.2
2.6-2.690.2058.2433926685997.5
2.69-2.790.1639.7733019659097.8
2.79-2.90.13211.8832014637497.7
2.9-3.030.10714.4930726610397.2
3.03-3.180.08118.6829248581697.2
3.18-3.350.062427821553197.2
3.35-3.560.04929.1125641520796
3.56-3.80.03935.7624230488895.7
3.8-4.110.03241.7622283454395.5
4.11-4.50.02846.1220949418795.4
4.5-5.030.02846.3518789377894.9
5.03-5.810.03242.1716384333994.1
5.81-7.120.02745.5314085282093.1
7.12-10.060.01863.2111076218992
10.060.01668.735559116684.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→38.49 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.547 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.272 5471 5.1 %RANDOM
Rwork0.212 ---
obs0.215 106831 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.31 Å2 / Biso mean: 31.54 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--1.42 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15122 0 7 462 15591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02115510
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210141
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.94321227
X-RAY DIFFRACTIONr_angle_other_deg0.959324621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96251967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67923.389714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71152285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.18515128
X-RAY DIFFRACTIONr_chiral_restr0.0940.22405
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023182
X-RAY DIFFRACTIONr_mcbond_it0.7981.59829
X-RAY DIFFRACTIONr_mcbond_other0.1991.53963
X-RAY DIFFRACTIONr_mcangle_it1.424215795
X-RAY DIFFRACTIONr_scbond_it2.22735681
X-RAY DIFFRACTIONr_scangle_it3.4774.55430
Refine LS restraints NCS

Ens-ID: 1 / Number: 3129 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.535
2BLOOSE POSITIONAL0.475
3CLOOSE POSITIONAL0.525
4DLOOSE POSITIONAL0.435
5ELOOSE POSITIONAL0.55
6FLOOSE POSITIONAL0.565
7GLOOSE POSITIONAL0.475
8HLOOSE POSITIONAL0.675
1ALOOSE THERMAL4.3310
2BLOOSE THERMAL5.0510
3CLOOSE THERMAL3.7610
4DLOOSE THERMAL10.4710
5ELOOSE THERMAL8.4410
6FLOOSE THERMAL5.0210
7GLOOSE THERMAL3.6910
8HLOOSE THERMAL9.0910
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 797 -
Rwork0.293 7065 -
all-7862 -
obs--97.75 %

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