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- PDB-7xto: Structure of ClA2 reveal the Mechanism of soil bacterial derived ... -

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Basic information

Entry
Database: PDB / ID: 7xto
TitleStructure of ClA2 reveal the Mechanism of soil bacterial derived chlorinase
Componentssoil bacterial derived chlorinase
KeywordsOXIDOREDUCTASE / chlorinase / SAM / ClDA / FDA / ANTIBIOTIC
Function / homology
Function and homology information


Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase N-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 ...Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase N-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1-DEAZA-ADENOSINE / SAM-dependent chlorinase/fluorinase
Similarity search - Component
Biological speciesUmezawaea tangerina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLiu, Y.H. / Liu, Y. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172299 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Expression, purification and structure determination of the chlorinase ClA2.
Authors: Liu, Y. / Zhang, H. / Xiao, H. / Li, Y. / Liu, Y.
History
DepositionMay 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: 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: soil bacterial derived chlorinase
C: soil bacterial derived chlorinase
D: soil bacterial derived chlorinase
B: soil bacterial derived chlorinase
E: soil bacterial derived chlorinase
F: soil bacterial derived chlorinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,88512
Polymers174,2886
Non-polymers1,5986
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.378, 104.423, 124.966
Angle α, β, γ (deg.)90.000, 108.880, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and (resid 6 through 7 or (resid 8...
d_2ens_1(chain "A" and (resid 6 through 7 or (resid 8...
d_3ens_1(chain "C" and (resid 6 through 7 or (resid 8...
d_4ens_1(chain "D" and (resid 6 through 7 or (resid 8...
d_5ens_1(chain "E" and (resid 6 through 7 or (resid 8...
d_6ens_1(chain "F" and (resid 6 through 10 or (resid 11...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROTHRTHRCB6 - 1706 - 170
d_12VALVALALAALACB180 - 198180 - 198
d_13VALVALVALVALCB209 - 215209 - 215
d_14ARGARGVALVALCB221 - 261221 - 261
d_15PROPROPROPROCB263263
d_16ALAALAALAALACB265265
d_171DA1DA1DA1DABJ301
d_21PROPROTHRTHRAA6 - 1706 - 170
d_22VALVALALAALAAA180 - 198180 - 198
d_23VALVALVALVALAA209 - 215209 - 215
d_24ARGARGVALVALAA221 - 261221 - 261
d_25PROPROPROPROAA263263
d_26ALAALAALAALAAA265265
d_271DA1DA1DA1DAAG301
d_31PROPROTHRTHRDC6 - 1706 - 170
d_32VALVALALAALADC180 - 198180 - 198
d_33VALVALVALVALDC209 - 215209 - 215
d_34ARGARGVALVALDC221 - 261221 - 261
d_35PROPROPROPRODC263263
d_36ALAALAALAALADC265265
d_371DA1DA1DA1DACH301
d_41PROPROTHRTHRBD6 - 1706 - 170
d_42VALVALVALVALBD180 - 261180 - 261
d_43PROPROPROPROBD263263
d_44ALAALAALAALABD265265
d_451DA1DA1DA1DADI301
d_51PROPROTHRTHREE6 - 1706 - 170
d_52VALVALALAALAEE180 - 198180 - 198
d_53VALVALVALVALEE209 - 215209 - 215
d_54ARGARGVALVALEE221 - 261221 - 261
d_55PROPROALAALAEE263 - 265263 - 265
d_561DA1DA1DA1DAEK301
d_61PROPROTHRTHRFF6 - 1706 - 170
d_62VALVALPROPROFF180 - 263180 - 263
d_63ALAALAALAALAFF265265
d_641DA1DA1DA1DAFL301

NCS oper:
IDCodeMatrixVector
1given(-0.999973920185, 0.00260441778828, -0.00673616791418), (0.00258427556829, 0.999992169312, 0.00299713773337), (0.00674392096418, 0.0029796514544, -0.999972820234)70.4508264496, 16.7981810391, 58.5649283565
2given(0.500752610024, 0.865588331945, -0.0019139371427), (0.865543208022, -0.50070095665, 0.0115545253831), (0.00904315219448, -0.00744255403764, -0.999931412542)-37.5814172946, -5.43434889138, 58.6912185834
3given(0.498806366186, -0.866700621681, -0.00471608202283), (-0.866710123786, -0.498812147041, 5.73697532702E-5), (-0.00240216140025, 0.00405885963563, -0.999988877578)-2.86337276628, 99.36283846, 59.1865377325
4given(-0.504013937106, -0.863667181086, -0.00699653614452), (0.86368451099, -0.504031876223, 0.000966037001515), (-0.00436081169391, -0.00555590378608, 0.999975057316)108.301560705, -22.2911990385, 0.430642706955
5given(-0.498751957588, 0.866672536345, -0.0111892603353), (-0.866688263173, -0.498825286624, -0.00497874508714), (-0.00989642762633, 0.00721444174761, 0.999925003463)73.3560710641, 82.3100748342, 0.547843311856

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Components

#1: Protein
soil bacterial derived chlorinase


Mass: 29047.953 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Umezawaea tangerina (bacteria) / Gene: CLV43_107328 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: A0A2T0T269
#2: Chemical
ChemComp-1DA / 1-DEAZA-ADENOSINE


Mass: 266.253 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H14N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 12% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.48→24.99 Å / Num. obs: 68111 / % possible obs: 86.85 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.41 Å2 / Rpim(I) all: 0.061 / Net I/σ(I): 6.8
Reflection shellResolution: 2.48→7.83 Å / Num. unique obs: 68111 / Rpim(I) all: 0.061

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q6K

2q6k


Resolution: 2.48→24.99 Å / SU ML: 0.3472 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.7769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3041 3335 4.9 %
Rwork0.2784 64776 -
obs0.2797 68111 86.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.51 Å2
Refinement stepCycle: LAST / Resolution: 2.48→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10319 0 114 239 10672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004810677
X-RAY DIFFRACTIONf_angle_d0.827814736
X-RAY DIFFRACTIONf_chiral_restr0.05271811
X-RAY DIFFRACTIONf_plane_restr0.00841914
X-RAY DIFFRACTIONf_dihedral_angle_d10.14781530
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONNCS constraints3.9011168445E-14
ens_1d_3CX-RAY DIFFRACTIONNCS constraints7.4872718366E-14
ens_1d_4DX-RAY DIFFRACTIONNCS constraints3.07520909491E-11
ens_1d_5EX-RAY DIFFRACTIONNCS constraints9.72557868612E-12
ens_1d_6FX-RAY DIFFRACTIONNCS constraints1.76104324551E-12
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.510.39341600.3582876X-RAY DIFFRACTION93.7
2.51-2.550.34491500.33142973X-RAY DIFFRACTION94.81
2.55-2.590.38261570.33742887X-RAY DIFFRACTION95.27
2.59-2.630.35521470.31192955X-RAY DIFFRACTION94.95
2.63-2.650.3496660.34061279X-RAY DIFFRACTION84.17
2.69-2.730.374850.30071850X-RAY DIFFRACTION92.81
2.73-2.780.31761510.30152938X-RAY DIFFRACTION94.38
2.78-2.840.32491560.30862937X-RAY DIFFRACTION94.1
2.84-2.90.34491610.30772873X-RAY DIFFRACTION93.99
2.9-2.960.34491450.30042917X-RAY DIFFRACTION93.98
2.96-3.040.30991570.28432903X-RAY DIFFRACTION94.33
3.04-3.120.3221270.26182936X-RAY DIFFRACTION93.84
3.12-3.210.28071470.27742896X-RAY DIFFRACTION93.34
3.21-3.320.30081500.2672883X-RAY DIFFRACTION93.35
3.32-3.430.29771310.27352878X-RAY DIFFRACTION92.64
3.43-3.570.31461350.27372897X-RAY DIFFRACTION92.21
3.57-3.730.24671300.25432893X-RAY DIFFRACTION92.22
3.73-3.840.3291880.26941634X-RAY DIFFRACTION88.58
3.94-4.170.27551280.25782716X-RAY DIFFRACTION89.77
4.17-4.490.23481430.23342714X-RAY DIFFRACTION87.5
4.49-4.940.2731610.2512786X-RAY DIFFRACTION89.49
4.94-5.650.29781460.28762787X-RAY DIFFRACTION89.5
5.65-7.090.30841690.29592781X-RAY DIFFRACTION89.04
7.09-24.990.32391450.27512587X-RAY DIFFRACTION81.16

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