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- PDB-7arp: Native L-2-haloacid dehalogenase from Zobellia galactanivorans -

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Basic information

Entry
Database: PDB / ID: 7arp
TitleNative L-2-haloacid dehalogenase from Zobellia galactanivorans
Components(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / Haloacid dehalogenase / Rossmann fold / cytoplasmic
Function / homology
Function and homology information


(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity
Similarity search - Function
L-2-Haloacid dehalogenase / : / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
PHOSPHATE ION / THIOCYANATE ION / (S)-2-haloacid dehalogenase
Similarity search - Component
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGrigorian, E. / Roret, T. / Czjzek, M. / Leblanc, C. / Delage, L.
CitationJournal: Protein Sci. / Year: 2022
Title: X-ray structure and mechanism of ZgHAD, a L-2-haloacid dehalogenase from the marine Flavobacterium Zobellia galactanivorans.
Authors: Grigorian, E. / Roret, T. / Czjzek, M. / Leblanc, C. / Delage, L.
History
DepositionOct 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (S)-2-haloacid dehalogenase
B: (S)-2-haloacid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0596
Polymers52,7532
Non-polymers3064
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-50 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.535, 68.826, 103.742
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
11(chain A and (resid 18 through 301 or resid 401))
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 18 through 301 or resid 401))A18 - 301
121(chain A and (resid 18 through 301 or resid 401))A401
211chain BB18 - 238

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Components

#1: Protein (S)-2-haloacid dehalogenase


Mass: 26376.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij) (bacteria)
Strain: DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij
Gene: dhlB, zobellia_4183 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0L7V6, (S)-2-haloacid dehalogenase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 31% PEG 3350, 0.33 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97986 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97986 Å / Relative weight: 1
ReflectionResolution: 1.78→45.03 Å / Num. obs: 41657 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Net I/av σ(I): 11.7 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.78-1.8213.70.7451.123640.8960.2080.774100
9.08-45.03110.0563800.9980.0170.05999.4

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YML

2yml


Resolution: 1.78→45.027 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 2092 5.03 %
Rwork0.1552 39491 -
obs0.1564 41583 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.42 Å2 / Biso mean: 26.5464 Å2 / Biso min: 11.84 Å2
Refinement stepCycle: final / Resolution: 1.78→45.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 16 473 3946
Biso mean--26.03 34.95 -
Num. residues----443
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2043X-RAY DIFFRACTION10.361TORSIONAL
12B2043X-RAY DIFFRACTION10.361TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.78-1.82140.32341240.26732621
1.8214-1.8670.28731270.21212599
1.867-1.91740.23371250.18222598
1.9174-1.97390.22651200.16862617
1.9739-2.03760.24751390.16132585
2.0376-2.11040.17531290.15892613
2.1104-2.19490.18591480.14762595
2.1949-2.29480.20091470.13832632
2.2948-2.41580.15031400.13742593
2.4158-2.56710.1791520.14662608
2.5671-2.76530.15911380.14552648
2.7653-3.04350.18761440.1472627
3.0435-3.48380.15771440.15022659
3.4838-4.38860.15341540.13882674
4.3886-45.0271612822
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)
10.7149-0.36650.12440.57420.41080.6074-0.0579-0.0077-0.1953-0.03710.0018-0.12160.09190.2024-0.00330.1380.0070.0270.1372-0.0010.1798-9.13212.081-8.491
20.50550.5988-0.27863.64450.50610.39220.0412-0.2353-0.06680.16530.0337-0.9917-0.09540.37790.07270.1795-0.01470.05410.18970.00290.30214.45529.242-18.909
30.14340.0832-0.15070.37110.31180.64630.10.0089-0.1313-0.0368-0.0399-0.04050.2087-0.08280.00010.1739-0.02060.01020.1463-0.00210.1351-11.70730.59-15.882
40.572-0.35590.38870.4058-0.00430.79290.15250.1760.1288-0.2494-0.0271-0.02050.0047-0.03630.00030.1876-0.020.02460.1467-0.00460.1326-11.80630.975-23.516
50.2785-0.43490.2521.0112-0.46340.24450.07310.1686-0.0047-0.7370.0283-0.24550.02330.25340.07470.3582-0.01570.1250.1982-0.01070.2501-0.97628.742-28.264
60.79220.6286-0.17490.61010.05360.38370.0042-0.0102-0.2195-0.045-0.1249-0.61610.15960.23170.02640.1790.02160.02640.1804-0.0060.2537-1.5796.29-9.735
70.2724-0.2171-0.02110.34840.28670.41260.08260.045-0.12190.1198-0.1127-0.0528-0.12970.01910.00010.1996-0.00550.0340.16330.0010.1995-13.8988.589-11.37
80.20440.0387-0.10350.19170.10670.13760.08470.1344-0.1151-0.2777-0.1449-0.03480.1828-0.054100.20420.02130.05010.1669-0.0220.1841-7.87.9-19.031
90.09740.08350.0710.08960.00820.2012-0.03780.1372-0.0048-0.30430.01730.1202-0.1085-0.1282-00.2224-0.0122-0.01040.22940.0050.2123-19.86617.741-15.972
100.2524-0.3103-0.03770.38060.02060.4023-0.0759-0.001-0.14370.0390.07860.10720.0305-0.07820.00010.1718-0.01290.02110.1607-0.00140.1992-20.71712.45-6.281
110.7252-0.2493-0.15950.69470.38380.5809-0.0559-0.0749-0.04230.21760.0809-0.08340.07280.1388-0.00010.16490.0104-0.01260.15720.00310.1436-9.31216.9920.39
120.5309-0.27420.77170.8032-0.43911.1348-0.00610.06380.1221-0.0221-0.0153-0.122-0.04110.01990.00010.1380.0040.0160.1476-0.00820.1445-11.18243.422-9.589
130.37750.3826-0.06280.46760.18440.77890.144-0.048-0.14680.1083-0.0657-0.06450.0292-0.1086-0.00010.1617-0.0051-0.0010.17820.00290.1903-12.04334.736-0.251
140.30840.26980.1470.28110.02780.35890.2072-0.1098-0.09270.1203-0.16670.09420.1493-0.05460.00010.2435-0.0397-0.00260.22370.0010.2463-3.65542.1773.789
150.30760.0642-0.2140.43210.10980.2717-0.20470.02240.4055-0.12040.0643-0.3832-0.2979-0.0428-0.00020.2363-0.01650.00020.20350.01230.2587-16.55460.847-14.668
160.4067-0.4705-0.11072.16350.37071.46010.05340.00740.0222-0.02530.0050.086-0.0326-0.12470.00020.12780.00080.01490.16970.00740.1541-23.71947.211-14.301
170.22090.1987-0.00060.21660.13540.497-0.01150.76620.251-0.7612-0.061-0.2404-0.23530.0186-0.01050.339-0.00560.03720.33050.04670.2183-17.91457.338-26.677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:22 )A7 - 22
2X-RAY DIFFRACTION2( CHAIN A AND RESID 23:37 )A23 - 37
3X-RAY DIFFRACTION3( CHAIN A AND RESID 38:55 )A38 - 55
4X-RAY DIFFRACTION4( CHAIN A AND RESID 56:76 )A56 - 76
5X-RAY DIFFRACTION5( CHAIN A AND RESID 77:94 )A77 - 94
6X-RAY DIFFRACTION6( CHAIN A AND RESID 95:111 )A95 - 111
7X-RAY DIFFRACTION7( CHAIN A AND RESID 112:123 )A112 - 123
8X-RAY DIFFRACTION8( CHAIN A AND RESID 124:141 )A124 - 141
9X-RAY DIFFRACTION9( CHAIN A AND RESID 142:155 )A142 - 155
10X-RAY DIFFRACTION10( CHAIN A AND RESID 156:179 )A156 - 179
11X-RAY DIFFRACTION11( CHAIN A AND RESID 180:227 )A180 - 227
12X-RAY DIFFRACTION12( CHAIN B AND RESID 7:55 )B7 - 55
13X-RAY DIFFRACTION13( CHAIN B AND RESID 56:76 )B56 - 76
14X-RAY DIFFRACTION14( CHAIN B AND RESID 77:94 )B77 - 94
15X-RAY DIFFRACTION15( CHAIN B AND RESID 95:111 )B95 - 111
16X-RAY DIFFRACTION16( CHAIN B AND RESID 112:211 )B112 - 211
17X-RAY DIFFRACTION17( CHAIN B AND RESID 212:227 )B212 - 227

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