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- PDB-7ccg: Crystal structure of ClA1, a kind of a chlorinase from soil bacteria -

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Basic information

Entry
Database: PDB / ID: 7ccg
TitleCrystal structure of ClA1, a kind of a chlorinase from soil bacteria
ComponentsDNA-directed RNA polymerase subunit delta
KeywordsCELL INVASION / Chlorinated enzyme / ClA1
Function / homology
Function and homology information


DNA-directed RNA polymerase complex
Similarity search - Function
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
Similarity search - Domain/homology
5'-CHLORO-5'-DEOXYADENOSINE / METHIONINE / DNA-directed RNA polymerase subunit delta
Similarity search - Component
Biological speciesStreptomyces albulus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOuyang, Z. / Li, Y.
Funding support1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of ClA1, a type of chlorinase from soil bacteria.
Authors: Miao, Y. / Yu, J. / Ouyang, Z. / Sun, H. / Li, Y.
History
DepositionJun 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7263
Polymers28,2911
Non-polymers4352
Water1,56787
1
A: DNA-directed RNA polymerase subunit delta
hetero molecules

A: DNA-directed RNA polymerase subunit delta
hetero molecules

A: DNA-directed RNA polymerase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1789
Polymers84,8733
Non-polymers1,3056
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9370 Å2
ΔGint-46 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.511, 96.511, 76.026
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

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Components

#1: Protein DNA-directed RNA polymerase subunit delta


Mass: 28291.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albulus (bacteria) / Gene: DC74_7605, SALB_08549, SALB_08560 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A059WF38
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5CD / 5'-CHLORO-5'-DEOXYADENOSINE


Mass: 285.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 289.15 K / Method: evaporation
Details: 0.1 M potassium chloride, 0.1 M sodium HEPES pH7.5, 15% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 22423 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 39.06 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.046 / Net I/σ(I): 39.19
Reflection shellResolution: 1.85→1.88 Å / Mean I/σ(I) obs: 1.555 / Num. unique obs: 1111 / CC1/2: 0.76 / Rrim(I) all: 0.854

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZ2

6rz2


Resolution: 1.85→5 Å / SU ML: 0.2253 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 26.7583
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2298 1975 8.81 %
Rwork0.2005 20443 -
obs0.2031 22418 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.07 Å2
Refinement stepCycle: LAST / Resolution: 1.85→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 28 87 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152017
X-RAY DIFFRACTIONf_angle_d1.30022769
X-RAY DIFFRACTIONf_chiral_restr0.0677334
X-RAY DIFFRACTIONf_plane_restr0.0095354
X-RAY DIFFRACTIONf_dihedral_angle_d6.7638279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.31691400.29021443X-RAY DIFFRACTION98.88
1.9-1.950.30751460.27151471X-RAY DIFFRACTION100
1.95-2.010.27821430.24661472X-RAY DIFFRACTION100
2.01-2.070.30571360.26451459X-RAY DIFFRACTION99.94
2.07-2.140.2721440.24091475X-RAY DIFFRACTION100
2.14-2.230.29631430.22331473X-RAY DIFFRACTION100
2.23-2.330.27571420.2281447X-RAY DIFFRACTION99.75
2.33-2.450.23871400.21441485X-RAY DIFFRACTION100
2.45-2.610.25921410.22511456X-RAY DIFFRACTION100
2.61-2.810.23841400.21281464X-RAY DIFFRACTION99.94
2.81-3.090.2331450.2171454X-RAY DIFFRACTION99.63
3.09-3.540.25151360.21291458X-RAY DIFFRACTION99.01
3.54-4.450.2051370.17371448X-RAY DIFFRACTION98.26
4.46-27.860.18761420.16891438X-RAY DIFFRACTION98.2

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