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- PDB-6uxu: X-ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing... -

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Basic information

Entry
Database: PDB / ID: 6uxu
TitleX-ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation
ComponentsChlorothalonil hydrolytic dehalogenase
KeywordsMETAL BINDING PROTEIN / hydrolase / Dehalogenase / Dechlorination / Zn-Dependent
Function / homologyMetallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Chlorothalonil hydrolytic dehalogenase
Function and homology information
Biological speciesOchrobactrum sp. CTN-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.962 Å
AuthorsCatlin, D.S. / Liu, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1412443 United States
National Science Foundation (NSF, United States)RCH & CHE 1462201 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis for the hydrolytic dehalogenation of the fungicide chlorothalonil.
Authors: Catlin, D.S. / Yang, X. / Bennett, B. / Holz, R.C. / Liu, D.
History
DepositionNov 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlorothalonil hydrolytic dehalogenase
B: Chlorothalonil hydrolytic dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6655
Polymers65,4692
Non-polymers1963
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-124 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.802, 105.182, 122.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chlorothalonil hydrolytic dehalogenase


Mass: 32734.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum sp. CTN-11 (bacteria) / Gene: chd / Production host: Escherichia coli (E. coli) / References: UniProt: E2JB04
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 6000, 100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.28167 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28167 Å / Relative weight: 1
ReflectionResolution: 1.96→50.019 Å / Num. obs: 50386 / % possible obs: 98 % / Redundancy: 7.2 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.631 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.027 / Net I/σ(I): 17.5
Reflection shellResolution: 1.96→1.98 Å / Num. unique obs: 2214 / CC1/2: 0.631

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data scaling
SOLVEphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.962→50.019 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 2399 4.94 %
Rwork0.1622 46169 -
obs0.1639 48568 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.65 Å2 / Biso mean: 24.2277 Å2 / Biso min: 6.89 Å2
Refinement stepCycle: final / Resolution: 1.962→50.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 3 402 5019
Biso mean--17.26 37.8 -
Num. residues----600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9624-2.00240.27881120.2423176363
2.0024-2.0460.23581100.2058217076
2.046-2.09360.22891280.188243986
2.0936-2.14590.23521460.1789266494
2.1459-2.2040.2171320.1713277597
2.204-2.26880.17811340.1637283399
2.2688-2.3420.20481310.16592824100
2.342-2.42580.19731630.1554277198
2.4258-2.52290.21141620.1503282999
2.5229-2.63770.19411420.15332871100
2.6377-2.77670.21571450.14962853100
2.7767-2.95070.17741440.15322857100
2.9507-3.17850.21291520.15752876100
3.1785-3.49830.19041310.1592914100
3.4983-4.00430.1881400.1536288899
4.0043-5.04420.16091600.1421283296
5.0442-50.0190.20831670.1857301098
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9020.79790.46971.20680.42651.596-0.0274-0.11990.0410.27040.2116-0.49340.0420.4223-0.08920.15980.0361-0.09590.26-0.07760.243249.896444.851549.0293
21.13610.34050.24231.62050.25161.2062-0.03770.07160.0433-0.0810.0759-0.1516-0.08680.2161-0.0240.0924-0.02460.01430.152-0.05120.104441.457847.496834.8723
32.25070.34090.05320.1473-0.31122.32150.0180.00080.00740.2225-0.05920.11220.0201-0.15960.04860.15820.0179-0.00040.1306-0.02160.118933.738837.531942.5901
41.1043-0.4077-0.55091.27490.84590.9864-0.0662-0.0833-0.03610.35170.06730.08790.12310.0131-0.00030.25110.03230.00210.12050.00780.087229.241749.744458.7547
52.03880.19480.02020.96880.35041.4562-0.0163-0.3684-0.06110.36970.0973-0.09250.004-0.0325-0.06180.16290.0113-0.01610.1680.00910.08833.331386.518154.4028
61.0786-0.05070.241.627-0.481.94050.0264-0.0814-0.0610.03570.0870.12990.0701-0.0861-0.10150.0522-0.0011-0.00120.10630.02990.098826.125380.111244.1084
73.09520.33520.01850.04960.18552.62850.01170.11280.07120.041-0.1025-0.1554-0.0120.04850.06990.119-0.0287-0.01710.09340.03210.117636.074891.503339.4754
81.8848-1.1651-0.59670.92170.06480.7803-0.04150.10630.2357-0.00520.0053-0.271-0.05170.04360.04520.1349-0.0578-0.02290.13040.01690.179249.941884.953641.5107
93.3917-0.6345-2.08992.76751.3124.2085-0.2555-0.0474-0.2176-0.05030.0362-0.31650.32150.21490.20040.1685-0.0203-0.00810.1230.03240.22357.39770.622541.7878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 67 )A28 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 182 )A68 - 182
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 217 )A183 - 217
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 327 )A218 - 327
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 85 )B28 - 85
6X-RAY DIFFRACTION6chain 'B' and (resid 86 through 182 )B86 - 182
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 217 )B183 - 217
8X-RAY DIFFRACTION8chain 'B' and (resid 218 through 285 )B218 - 285
9X-RAY DIFFRACTION9chain 'B' and (resid 286 through 327 )B286 - 327

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