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- PDB-4k2a: Crystal structure of haloalkane dehalogenase DbeA from Bradyrhizo... -

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Basic information

Entry
Database: PDB / ID: 4k2a
TitleCrystal structure of haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Structural Genomics / Enzyme Function Initiative / Structure 2 Function Project / S2F / two domain organization / dimer catalytic pentad / halogen binding
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
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
ACETATE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesBradyrhizobium elkanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsPrudnikova, T. / Chaloupkova, R. / Rezacova, P. / Mozga, T. / Koudelakova, T. / Sato, Y. / Kuty, M. / Nagata, Y. / Damborsky, J. / Kuta Smatanova, I. / Structure 2 Function Project (S2F)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites.
Authors: Chaloupkova, R. / Prudnikova, T. / Rezacova, P. / Prokop, Z. / Koudelakova, T. / Daniel, L. / Brezovsky, J. / Ikeda-Ohtsubo, W. / Sato, Y. / Kuty, M. / Nagata, Y. / Kuta Smatanova, I. / Damborsky, J.
History
DepositionApr 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
C: Haloalkane dehalogenase
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,34615
Polymers130,8854
Non-polymers46111
Water13,493749
1
A: Haloalkane dehalogenase
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5846
Polymers65,4432
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-63 kcal/mol
Surface area21260 Å2
MethodPISA
2
B: Haloalkane dehalogenase
C: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7619
Polymers65,4432
Non-polymers3197
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-62 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.702, 121.888, 161.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 297
2115B1 - 297
3115C1 - 297
4115D1 - 297

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Components

#1: Protein
Haloalkane dehalogenase /


Mass: 32721.256 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium elkanii (bacteria) / Strain: USDA94 / Gene: dbeA, dhaA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E2RV62, haloalkane dehalogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris HCl, 20% (w/v) PEG 3350 or 4000 and 150 mM calcium acetate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2008 / Details: mirrors
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→29.71 Å / Num. all: 79384 / Num. obs: 73280 / % possible obs: 92.31 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.64
Reflection shellResolution: 2.201→2.258 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.3 / % possible all: 62.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 2.2→29.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.561 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20858 2945 5 %RANDOM
Rwork0.14791 ---
obs0.1509 55927 92.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0.05 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9048 0 20 749 9817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0199499
X-RAY DIFFRACTIONr_bond_other_d0.0010.028987
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.95112964
X-RAY DIFFRACTIONr_angle_other_deg0.888320619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54151228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50322.266428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.162151447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1621585
X-RAY DIFFRACTIONr_chiral_restr0.10.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110932
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022303
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_it0.8270.9024774
X-RAY DIFFRACTIONr_mcbond_other0.820.9024772
X-RAY DIFFRACTIONr_mcangle_it1.3721.3455974
X-RAY DIFFRACTIONr_mcangle_other1.3052.1045975
X-RAY DIFFRACTIONr_scbond_it1.1891.0344725
X-RAY DIFFRACTIONr_scbond_other1.1761.5494726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8932.2666967
X-RAY DIFFRACTIONr_long_range_B_refined5.00412.18511311
X-RAY DIFFRACTIONr_long_range_B_other4.90311.8611083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1139medium positional0.150.5
1139medium positional0.170
1139medium positional0.150
1139medium positional0.180
986loose positional0.435
986loose positional0.460.01
986loose positional0.410
986loose positional0.440
1139medium thermal0.582
1139medium thermal0.60
1139medium thermal0.580
1139medium thermal0.550
986loose thermal0.7710
986loose thermal0.80.01
986loose thermal0.840
986loose thermal0.720
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 128 -
Rwork0.172 2690 -
obs--60.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.93492.60033.85292.07410.83743.94720.14340.0475-0.2450.2017-0.0072-0.03070.2936-0.0719-0.13620.1649-0.00740.00620.12410.02170.168634.7946-74.752944.4892
21.46930.09162.10210.02670.0913.1119-0.0165-0.0062-0.0324-0.0113-0.0571-0.02740.02670.08790.07360.17850.02690.00370.13380.05180.269141.9295-69.968444.7072
30.33160.22680.28460.24480.01090.78790.0333-0.0285-0.07320.00180.0133-0.021-0.0148-0.029-0.04660.15770.02110.01190.10270.02710.204738.6192-60.397643.208
40.61130.08570.50710.19520.61082.0117-0.00340.1116-0.0245-0.0395-0.03860.0182-0.1047-0.06960.0420.19220.0220.03320.06710.02690.199335.834-49.201236.9141
51.07830.29650.83141.6265-0.92872.1964-0.0061-0.27810.14390.00770.01430.1209-0.171-0.2211-0.00810.11520.06110.03760.1763-0.04510.155225.9087-44.740755.5262
64.31030.79580.52653.8065-0.2650.10350.1212-0.53210.2052-0.0645-0.15410.07860.024-0.07940.03280.12770.0110.04620.2288-0.00090.146518.6131-59.550450.3718
70.86130.3142-0.23930.6948-0.25750.46-0.0231-0.16360.10490.00090.0595-0.0066-0.0725-0.0986-0.03650.13150.02390.02110.15280.00080.153235.5923-49.615750.9413
81.38670.4924-0.65770.6683-0.1670.3219-0.01540.0350.1279-0.12350.07630.0683-0.0137-0.0182-0.06090.15830.0296-0.00220.11960.01890.180427.9316-48.634232.8777
93.66981.0379-0.5580.91210.64821.1642-0.11990.18460.2601-0.1190.09030.1522-0.04330.00470.02960.16390.013-0.00780.12570.05710.156428.2852-48.858529.8555
100.3449-0.09680.05040.09940.36612.03370.0367-0.0196-0.1219-0.03310.02710.0356-0.14980.083-0.06370.1513-0.00080.01430.11650.02450.199829.8622-62.320229.4414
114.52122.3192-4.71331.1924-2.36256.34750.0848-0.18130.01260.044-0.09560.0078-0.31650.04950.01080.20280.03570.00550.0534-0.04070.1852-8.4334-19.040146.5749
125.0774-4.24365.95786.5689-3.0588.218-0.41790.14450.14060.24830.05140.2061-0.59230.27270.36650.19960.00210.02020.01940.01880.0703-7.506-20.47132.347
130.31490.084-0.0750.0325-0.06060.8167-0.0151-0.05460.0345-0.0143-0.00130.0331-0.00910.04250.01640.16480.02060.00580.0912-0.02040.2106-5.9864-28.773243.6116
141.0614-0.26910.40630.7874-0.75970.7625-0.06620.0727-0.0369-0.03530.0524-0.01460.0325-0.01280.01380.17850.02330.02510.0866-0.0110.1887-4.3154-41.129438.2515
151.8055-0.5253-0.04062.04862.0212.13080.0781-0.0973-0.0050.04640.193-0.24620.06730.1763-0.27110.12310.07990.00210.15660.05830.17418.5672-47.001451.7571
161.1372-0.70250.35645.5166-1.81880.6865-0.2513-0.2633-0.13870.16830.3581-0.1361-0.0223-0.0903-0.10680.13330.0913-0.06960.2149-0.02980.2514.322-40.237162.8244
173.58812.7412-4.23382.3159-2.74586.1154-0.0744-0.0484-0.0479-0.024-0.067-0.02420.20050.04150.14140.1220.0422-0.01140.1650.01390.162611.1455-34.020951.1936
180.9352-0.46890.03130.31710.0750.1865-0.0562-0.21960.02850.03930.0830.01350.00880.0638-0.02680.14450.00050.01060.1886-0.03810.12253.7883-31.94754.998
190.80070.3579-0.06910.51-0.23790.502-0.04990.0178-0.0751-0.06880.0355-0.04830.05970.06010.01430.16330.01940.01080.1004-0.00540.18221.4746-38.98334.021
201.2168-0.1977-1.53410.40132.087611.13320.17270.32430.12610.0304-0.0269-0.00010.0403-0.2719-0.14580.16820.0190.02820.18220.03840.2127-6.0878-26.214320.5718
211.07681.20411.73471.60480.478811.10470.0626-0.0659-0.05110.0445-0.1249-0.07290.22630.12140.06230.16090.01870.01190.1398-0.00160.167621.5195-36.69311.3938
221.19720.2427-1.2680.14470.26114.2227-0.15920.0981-0.293-0.01180.0095-0.09420.2736-0.04970.14970.18170.00630.04340.1301-0.04010.191518.4061-34.55892.9439
230.92490.2412-0.28630.2486-0.12970.3587-0.03790.1371-0.06530.0020.0105-0.01670.0528-0.00510.02750.1673-0.01180.00440.1203-0.04170.172713.0172-26.2375.2299
241.26471.5229-0.01871.85220.08250.74660.02830.00910.03210.028-0.00340.0583-0.0977-0.0472-0.02490.16580.00360.0110.1149-0.00510.160510.5834-7.71539.677
252.4232-1.8263-0.24132.8134-1.15461.26890.07810.05930.06570.0479-0.0971-0.0859-0.10530.05660.0190.1576-0.03780.00770.13990.00490.154926.4405-5.3012.0042
261.2958-0.4571-0.29211.9528-0.17942.0810.1325-0.18720.1311-0.09570.05630.053-0.14060.2807-0.18890.1336-0.0379-0.00660.1272-0.02060.17227.3113-14.73416.8696
271.3476-0.2922-0.11950.6402-0.0160.3702-0.06150.19710.0573-0.07550.0525-0.1201-0.01920.02430.00910.1507-0.02570.00770.141-0.00540.144722.5002-13.50731.4587
281.3406-0.015-0.22870.0076-0.05840.7043-0.02580.06290.09390.02130.02240.0033-0.0906-0.19420.00340.16380.0048-0.02980.13620.00880.16133.5376-13.901711.9151
293.80311.1851.70970.99770.04611.6442-0.0843-0.073-0.01730.05260.08470.0241-0.073-0.1423-0.00050.13830.00640.00740.1233-0.02550.14562.2544-13.828517.6123
300.98680.4048-0.65590.1845-0.27010.4411-0.14820.121-0.058-0.07610.0866-0.06350.08-0.07110.06160.1885-0.03620.00190.1461-0.01060.1733.1712-28.397119.1332
312.07050.95091.80040.65971.90877.7580.0458-0.05810.12620.0136-0.05520.1081-0.1081-0.17140.00940.16210.0167-0.00980.13780.01620.174110.3867-51.25989.881
321.1122-0.01181.26660.0542-0.03051.4536-0.07290.2370.16910.0116-0.09190.0161-0.10640.28150.16470.18630.00650.00290.23150.07810.144616.8581-54.02637.8169
331.05520.11480.6980.28230.26881.13180.03210.10210.04330.0074-0.0570.0297-0.01680.04250.02490.13570.0211-0.00860.15930.0640.144114.9753-61.87976.6975
341.77281.3214-0.67891.1792-1.07282.17760.07740.170.05560.0624-0.0080.1031-0.02870.2418-0.06940.12160.00480.00480.23140.0090.156524.9743-67.49155.8904
351.60351.4496-2.58141.4504-2.37374.29590.0425-0.164-0.0881-0.0602-0.0727-0.11140.08370.19930.03020.223-0.0454-0.07550.13950.03240.167116.4501-87.00588.7283
361.9909-0.63-0.84092.00560.86752.86260.07230.0029-0.1424-0.0001-0.05260.13070.2692-0.2375-0.01970.1493-0.0691-0.08450.14340.03250.13812.6127-81.24453.6355
370.23860.0456-0.03991.3769-0.51544.5708-0.08-0.1314-0.16040.11710.22740.01510.2609-0.4036-0.14740.1371-0.0120.02670.2170.08030.17583.602-72.738919.2753
380.5547-0.14370.33030.5732-0.04730.73220.09030.0852-0.09-0.042-0.01360.06410.110.0491-0.07670.12380.0067-0.01210.17260.00180.10715.2145-73.48324.4317
393.21290.9498-1.20040.4859-0.25372.2686-0.0207-0.0223-0.07950.0120.09240.00780.26810.1296-0.07170.14490.03580.00170.13230.03390.143425.8297-77.706617.6646
400.6680.28760.62370.1850.16740.7648-0.04680.14890.04110.00640.0980.0616-0.04360.0456-0.05110.145-0.0210.00170.15590.04540.184623.069-63.498520.9922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 10
2X-RAY DIFFRACTION2A11 - 29
3X-RAY DIFFRACTION3A30 - 117
4X-RAY DIFFRACTION4A118 - 134
5X-RAY DIFFRACTION5A135 - 169
6X-RAY DIFFRACTION6A170 - 185
7X-RAY DIFFRACTION7A186 - 231
8X-RAY DIFFRACTION8A232 - 253
9X-RAY DIFFRACTION9A254 - 271
10X-RAY DIFFRACTION10A272 - 301
11X-RAY DIFFRACTION11B6 - 25
12X-RAY DIFFRACTION12B26 - 34
13X-RAY DIFFRACTION13B35 - 114
14X-RAY DIFFRACTION14B115 - 138
15X-RAY DIFFRACTION15B139 - 152
16X-RAY DIFFRACTION16B153 - 166
17X-RAY DIFFRACTION17B167 - 177
18X-RAY DIFFRACTION18B178 - 210
19X-RAY DIFFRACTION19B211 - 289
20X-RAY DIFFRACTION20B290 - 296
21X-RAY DIFFRACTION21C6 - 10
22X-RAY DIFFRACTION22C11 - 26
23X-RAY DIFFRACTION23C27 - 120
24X-RAY DIFFRACTION24C121 - 146
25X-RAY DIFFRACTION25C147 - 167
26X-RAY DIFFRACTION26C168 - 183
27X-RAY DIFFRACTION27C184 - 219
28X-RAY DIFFRACTION28C220 - 252
29X-RAY DIFFRACTION29C253 - 271
30X-RAY DIFFRACTION30C272 - 304
31X-RAY DIFFRACTION31D6 - 12
32X-RAY DIFFRACTION32D13 - 34
33X-RAY DIFFRACTION33D35 - 103
34X-RAY DIFFRACTION34D104 - 129
35X-RAY DIFFRACTION35D130 - 146
36X-RAY DIFFRACTION36D147 - 169
37X-RAY DIFFRACTION37D170 - 184
38X-RAY DIFFRACTION38D185 - 239
39X-RAY DIFFRACTION39D240 - 271
40X-RAY DIFFRACTION40D272 - 297

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