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- PDB-2qlc: The crystal structure of DNA repair protein RadC from Chlorobium ... -

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Basic information

Entry
Database: PDB / ID: 2qlc
TitleThe crystal structure of DNA repair protein RadC from Chlorobium tepidum TLS
ComponentsDNA repair protein radC homolog
KeywordsDNA BINDING PROTEIN / DNA repair protein / RadC / MCSG / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


metallopeptidase activity / metal ion binding
Similarity search - Function
Uncharacterised protein family UPF0758 / Uncharacterised protein family UPF0758, conserved site / RadC-like JAB domain / RadC-like JAB domain / Uncharacterized protein family UPF0758 signature. / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / RuvA domain 2-like / MPN domain / MPN domain profile. ...Uncharacterised protein family UPF0758 / Uncharacterised protein family UPF0758, conserved site / RadC-like JAB domain / RadC-like JAB domain / Uncharacterized protein family UPF0758 signature. / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / RuvA domain 2-like / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0758 protein CT0611
Similarity search - Component
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, R. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of DNA repair protein RadC from Chlorobium tepidum TLS.
Authors: Zhang, R. / Duggan, E. / Clancy, S. / Joachimiak, A.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ... BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). AUTHORS STATE THAT A MONOMER IS PROBABLY THE BIOLOGICAL UNIT OF THIS PROTEIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein radC homolog
B: DNA repair protein radC homolog
C: DNA repair protein radC homolog
D: DNA repair protein radC homolog
E: DNA repair protein radC homolog
F: DNA repair protein radC homolog
G: DNA repair protein radC homolog
H: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)114,3808
Polymers114,3808
Non-polymers00
Water4,125229
1
A: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: DNA repair protein radC homolog


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.434, 95.959, 192.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIt seems that this protein existed as monomer.

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Components

#1: Protein
DNA repair protein radC homolog


Mass: 14297.465 Da / Num. of mol.: 8 / Fragment: Residues 97-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS, DSM 12025 / Gene: radC, CT0611 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KES1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulfate, 0.1M Tris-HCl, 20% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 51740 / Num. obs: 49789 / % possible obs: 96.23 % / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 21.68
Reflection shellResolution: 2.3→2.359 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.81 / % possible all: 0.9291

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→48 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.142 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.351 / ESU R Free: 0.261
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27385 2667 5.1 %RANDOM
Rwork0.21586 ---
obs0.2188 49789 98.76 %-
all-49789 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.45 Å20 Å2
3----1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.045 Å0.042 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.3→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 0 229 8181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0218109
X-RAY DIFFRACTIONr_bond_other_d0.0010.025492
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.94810963
X-RAY DIFFRACTIONr_angle_other_deg0.964313454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2155987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26223.989371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8151485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6911548
X-RAY DIFFRACTIONr_chiral_restr0.0890.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021585
X-RAY DIFFRACTIONr_nbd_refined0.210.21728
X-RAY DIFFRACTIONr_nbd_other0.2030.25576
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23870
X-RAY DIFFRACTIONr_nbtor_other0.0920.24361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2091.56489
X-RAY DIFFRACTIONr_mcbond_other0.1571.51998
X-RAY DIFFRACTIONr_mcangle_it1.41128040
X-RAY DIFFRACTIONr_scbond_it2.03133494
X-RAY DIFFRACTIONr_scangle_it3.0624.52923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 173 -
Rwork0.258 3432 -
obs--92.91 %
Refinement TLS params.Method: refined / Origin x: 43.548 Å / Origin y: -2.221 Å / Origin z: 23.143 Å
111213212223313233
T-0.1144 Å2-0.0252 Å2-0.0243 Å2-0.0082 Å20.0133 Å2---0.1306 Å2
L0.2353 °2-0.0326 °20.0733 °2-0.4842 °20.1455 °2--0.375 °2
S-0.0026 Å °-0.0385 Å °0.0188 Å °0.0485 Å °-0.0044 Å °-0.0357 Å °0.0237 Å °-0.0399 Å °0.007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 401 - 40
2X-RAY DIFFRACTION1AA41 - 8041 - 80
3X-RAY DIFFRACTION1AA81 - 12681 - 126
4X-RAY DIFFRACTION1BB2 - 402 - 40
5X-RAY DIFFRACTION1BB41 - 8041 - 80
6X-RAY DIFFRACTION1BB81 - 12581 - 125
7X-RAY DIFFRACTION1CC2 - 402 - 40
8X-RAY DIFFRACTION1CC41 - 8041 - 80
9X-RAY DIFFRACTION1CC81 - 12681 - 126
10X-RAY DIFFRACTION1DD4 - 404 - 40
11X-RAY DIFFRACTION1DD41 - 8041 - 80
12X-RAY DIFFRACTION1DD81 - 12581 - 125
13X-RAY DIFFRACTION1EE3 - 403 - 40
14X-RAY DIFFRACTION1EE41 - 8041 - 80
15X-RAY DIFFRACTION1EE81 - 12681 - 126
16X-RAY DIFFRACTION1FF1 - 401 - 40
17X-RAY DIFFRACTION1FF41 - 8041 - 80
18X-RAY DIFFRACTION1FF81 - 12681 - 126
19X-RAY DIFFRACTION1GG3 - 403 - 40
20X-RAY DIFFRACTION1GG41 - 8041 - 80
21X-RAY DIFFRACTION1GG81 - 12681 - 126
22X-RAY DIFFRACTION1HH3 - 403 - 40
23X-RAY DIFFRACTION1HH41 - 8041 - 80
24X-RAY DIFFRACTION1HH81 - 12681 - 126

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