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- PDB-7avr: The tetrameric structure of haloalkane dehalogenase DpaA from Par... -

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Basic information

Entry
Database: PDB / ID: 7avr
TitleThe tetrameric structure of haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2
ComponentsHaloalkane dehalogenase 1
KeywordsHYDROLASE / Haloalkane dehalogenase / enzyme / tetramer
Function / homologyEpoxide hydrolase-like / catalytic activity / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Haloalkane dehalogenase 1
Function and homology information
Biological speciesParaglaciecola agarilytica NO2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMazur, A. / Kolenko, P. / Prudnikova, T. / Grinkevich, P. / Kuta Smatanova, I.
Funding support Czech Republic, Germany, 7items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic17-24321S Czech Republic
German Research Foundation (DFG)DAAD-16-09 Germany
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000441 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000778 Czech Republic
European Regional Development FundLM2015047 Czech Republic
European Regional Development FundLM2018121 Czech Republic
Ministry of Education (MoE, Czech Republic)CZ.02.1.01/0.0/0.0/16_026/0008451 Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2.
Authors: Mazur, A. / Prudnikova, T. / Grinkevich, P. / Mesters, J.R. / Mrazova, D. / Chaloupkova, R. / Damborsky, J. / Kuty, M. / Kolenko, P. / Kuta Smatanova, I.
History
DepositionNov 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase 1
B: Haloalkane dehalogenase 1
C: Haloalkane dehalogenase 1
D: Haloalkane dehalogenase 1
E: Haloalkane dehalogenase 1
F: Haloalkane dehalogenase 1
G: Haloalkane dehalogenase 1
H: Haloalkane dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,85726
Polymers276,2198
Non-polymers63818
Water36,1742008
1
A: Haloalkane dehalogenase 1
B: Haloalkane dehalogenase 1
C: Haloalkane dehalogenase 1
D: Haloalkane dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,32210
Polymers138,1094
Non-polymers2136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-113 kcal/mol
Surface area42190 Å2
MethodPISA
2
E: Haloalkane dehalogenase 1
F: Haloalkane dehalogenase 1
G: Haloalkane dehalogenase 1
H: Haloalkane dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,53516
Polymers138,1094
Non-polymers42512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-165 kcal/mol
Surface area42210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.385, 155.506, 155.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11F-682-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILETHRTHRAA3 - 2993 - 299
21ILEILETHRTHRBB3 - 2993 - 299
12ILEILETHRTHRAA3 - 2993 - 299
22ILEILETHRTHRCC3 - 2993 - 299
13ILEILEPHEPHEAA3 - 2983 - 298
23ILEILEPHEPHEDD3 - 2983 - 298
14ILEILETHRTHRAA3 - 2993 - 299
24ILEILETHRTHREE3 - 2993 - 299
15ILEILEPHEPHEAA3 - 2983 - 298
25ILEILEPHEPHEFF3 - 2983 - 298
16ILEILETHRTHRAA3 - 2993 - 299
26ILEILETHRTHRGG3 - 2993 - 299
17ILEILEILEILEAA3 - 3013 - 301
27ILEILEILEILEHH3 - 3013 - 301
18ILEILETHRTHRBB3 - 2993 - 299
28ILEILETHRTHRCC3 - 2993 - 299
19ILEILEPHEPHEBB3 - 2983 - 298
29ILEILEPHEPHEDD3 - 2983 - 298
110ILEILEMETMETBB3 - 3003 - 300
210ILEILEMETMETEE3 - 3003 - 300
111ILEILEPHEPHEBB3 - 2983 - 298
211ILEILEPHEPHEFF3 - 2983 - 298
112ILEILETHRTHRBB3 - 2993 - 299
212ILEILETHRTHRGG3 - 2993 - 299
113ILEILETHRTHRBB3 - 2993 - 299
213ILEILETHRTHRHH3 - 2993 - 299
114ILEILEPHEPHECC3 - 2983 - 298
214ILEILEPHEPHEDD3 - 2983 - 298
115ILEILETHRTHRCC3 - 2993 - 299
215ILEILETHRTHREE3 - 2993 - 299
116THRTHRPHEPHECC2 - 2982 - 298
216THRTHRPHEPHEFF2 - 2982 - 298
117THRTHRMETMETCC2 - 3002 - 300
217THRTHRMETMETGG2 - 3002 - 300
118ILEILETHRTHRCC3 - 2993 - 299
218ILEILETHRTHRHH3 - 2993 - 299
119ILEILEPHEPHEDD3 - 2983 - 298
219ILEILEPHEPHEEE3 - 2983 - 298
120ILEILEPHEPHEDD3 - 2983 - 298
220ILEILEPHEPHEFF3 - 2983 - 298
121ILEILEPHEPHEDD3 - 2983 - 298
221ILEILEPHEPHEGG3 - 2983 - 298
122ILEILEPHEPHEDD3 - 2983 - 298
222ILEILEPHEPHEHH3 - 2983 - 298
123ILEILEPHEPHEEE3 - 2983 - 298
223ILEILEPHEPHEFF3 - 2983 - 298
124ILEILETHRTHREE3 - 2993 - 299
224ILEILETHRTHRGG3 - 2993 - 299
125ILEILETHRTHREE3 - 2993 - 299
225ILEILETHRTHRHH3 - 2993 - 299
126THRTHRPHEPHEFF2 - 2982 - 298
226THRTHRPHEPHEGG2 - 2982 - 298
127ILEILEPHEPHEFF3 - 2983 - 298
227ILEILEPHEPHEHH3 - 2983 - 298
128ILEILETHRTHRGG3 - 2993 - 299
228ILEILETHRTHRHH3 - 2993 - 299

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Haloalkane dehalogenase 1 / Haloalkane Dehalogenase DpaA


Mass: 34527.328 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraglaciecola agarilytica NO2 (bacteria)
Gene: dhmA1, GAGA_3124 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K6XNL5, haloalkane dehalogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2008 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 53.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Na HEPES, 4% w/v PEG 400, 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2→47.44 Å / Num. obs: 191831 / % possible obs: 100 % / Redundancy: 1.79 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0179 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 59344 / CC1/2: 0.601 / Rrim(I) all: 0.0161 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xt0

2xt0


Resolution: 2→47.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20586 9496 4.9 %RANDOM
Rwork0.17649 ---
obs0.17798 182376 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: 27.229 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0 Å2
2--0.25 Å20 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 2→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18745 0 18 2008 20771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01919269
X-RAY DIFFRACTIONr_bond_other_d00.0217587
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.95726149
X-RAY DIFFRACTIONr_angle_other_deg3.875340893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12752395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80324.839899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.557153181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6431580
X-RAY DIFFRACTIONr_chiral_restr0.1220.22808
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02121591
X-RAY DIFFRACTIONr_gen_planes_other0.0170.023917
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_it3.292.6669562
X-RAY DIFFRACTIONr_mcbond_other3.292.6659561
X-RAY DIFFRACTIONr_mcangle_it4.1193.98811945
X-RAY DIFFRACTIONr_mcangle_other4.1193.98911946
X-RAY DIFFRACTIONr_scbond_it3.4542.8169707
X-RAY DIFFRACTIONr_scbond_other3.4532.8169708
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3534.1614199
X-RAY DIFFRACTIONr_long_range_B_refined6.24232.1722958
X-RAY DIFFRACTIONr_long_range_B_other6.03831.79322267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A192960.1
12B192960.1
21A194000.1
22C194000.1
31A193520.09
32D193520.09
41A192780.1
42E192780.1
51A193240.1
52F193240.1
61A194140.09
62G194140.09
71A197520.08
72H197520.08
81B192460.1
82C192460.1
91B191000.1
92D191000.1
101B196720.08
102E196720.08
111B190760.1
112F190760.1
121B193740.09
122G193740.09
131B190920.1
132H190920.1
141C193580.09
142D193580.09
151C193240.1
152E193240.1
161C193300.1
162F193300.1
171C197940.08
172G197940.08
181C191940.1
182H191940.1
191D192160.09
192E192160.09
201D197800.06
202F197800.06
211D193500.08
212G193500.08
221D192600.09
222H192600.09
231E192480.09
232F192480.09
241E194260.09
242G194260.09
251E192000.1
252H192000.1
261F193140.09
262G193140.09
271F192700.1
272H192700.1
281G192800.1
282H192800.1
LS refinement shellResolution: 2→2.051 Å
RfactorNum. reflection% reflection
Rfree0.118 673 -
Rwork0.088 13173 -
obs--98.07 %

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