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- PDB-5f54: Structure of RecJ complexed with dTMP -

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Basic information

Entry
Database: PDB / ID: 5f54
TitleStructure of RecJ complexed with dTMP
ComponentsSingle-stranded-DNA-specific exonuclease
KeywordsDNA BINDING PROTEIN / RecF pathway / DNA end resection / two-metal-ion catalysis / single-strand-DNA
Function / homology
Function and homology information


5'-3' exonuclease activity / DNA recombination / nucleic acid binding / DNA repair / metal ion binding
Similarity search - Function
Bacterial RecJ exonuclease / : / RecJ C-terminal domain, Deinococci / inorganic pyrophosphatase (n-terminal core) - #30 / RecJ, OB domain / RecJ OB domain / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family ...Bacterial RecJ exonuclease / : / RecJ C-terminal domain, Deinococci / inorganic pyrophosphatase (n-terminal core) - #30 / RecJ, OB domain / RecJ OB domain / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / THYMIDINE-5'-PHOSPHATE / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHua, Y. / Zhao, Y. / Cheng, K.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Program of China2015CB910600 China
Zhejiang Provincial Natural Science Foundation for Outstanding Young ScientistsLR16C050002 China
National Natural Science Foundation of China31500656 China
CitationJournal: Elife / Year: 2016
Title: Structural basis for DNA 5 -end resection by RecJ
Authors: Cheng, K. / Xu, H. / Chen, X. / Wang, L. / Tian, B. / Zhao, Y. / Hua, Y.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single-stranded-DNA-specific exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4644
Polymers76,0321
Non-polymers4323
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-17 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.530, 106.530, 161.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Single-stranded-DNA-specific exonuclease


Mass: 76031.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: recJ / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rossetta / References: UniProt: D0EM60
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.49 Å3/Da / Density % sol: 64.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, MnCl2, Li2SO4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.04
ReflectionResolution: 2.7→30 Å / Num. obs: 29475 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.058 / Χ2: 0.991 / Net I/σ(I): 27.02 / Num. measured all: 264098
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.7-2.770.9280.641419547215221410.67999.5
2.77-2.850.930.5284.9719730212421230.559100
2.85-2.930.9660.3586.9819173206220610.379100
2.93-3.020.980.2898.2218654200620060.306100
3.02-3.120.9880.21110.918095195019490.22399.9
3.12-3.230.9930.15414.3417612189318930.163100
3.23-3.350.9960.11318.3416771180918090.12100
3.35-3.490.9970.08822.8415984173217310.09499.9
3.49-3.640.9980.0728.6415347168816880.074100
3.64-3.820.9990.05533.1114757162716260.05999.9
3.82-4.030.9990.04440.2213824153415340.046100
4.03-4.270.9990.03845.312953145114510.04100
4.27-4.560.9990.03550.0312066137513750.038100
4.56-4.930.9990.03352.0811093129012890.03599.9
4.93-5.40.9990.03451.5310110119311920.03699.9
5.4-6.040.9990.03353.619007107710770.035100
6.04-6.970.9990.0356.8782379629610.03299.9
6.97-8.540.9990.02758.3265388348190.02998.2
8.54-12.080.9990.02753.9633896535180.02979.3
12.080.9990.0344.3212113952310.03358.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata processing
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZXP

2zxp


Resolution: 2.7→29.288 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.76 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.252 1511 5.13 %
Rwork0.2061 --
obs0.2088 29475 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5262 0 23 12 5297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125417
X-RAY DIFFRACTIONf_angle_d1.0857391
X-RAY DIFFRACTIONf_dihedral_angle_d19.9271986
X-RAY DIFFRACTIONf_chiral_restr0.048837
X-RAY DIFFRACTIONf_plane_restr0.007980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7014-2.78850.361490.35432518X-RAY DIFFRACTION94
2.7885-2.88810.3771610.3262513X-RAY DIFFRACTION94
2.8881-3.00360.30611150.31332517X-RAY DIFFRACTION96
3.0036-3.14010.3111210.29142554X-RAY DIFFRACTION95
3.1401-3.30540.32371340.26252540X-RAY DIFFRACTION95
3.3054-3.51210.27741450.24162535X-RAY DIFFRACTION95
3.5121-3.78270.29021370.21252557X-RAY DIFFRACTION95
3.7827-4.16220.22531330.18362561X-RAY DIFFRACTION95
4.1622-4.76180.21111320.16362588X-RAY DIFFRACTION95
4.7618-5.98940.21751570.17742597X-RAY DIFFRACTION94
5.9894-27.67010.23231200.16892463X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: -57.9221 Å / Origin y: 12.4085 Å / Origin z: 3.4464 Å
111213212223313233
T0.4183 Å2-0.0728 Å2-0.0437 Å2-0.4245 Å20.0093 Å2--0.4691 Å2
L0.6395 °2-0.5179 °2-0.9469 °2-1.5111 °21.05 °2--2.5623 °2
S-0.0895 Å °0.1527 Å °0.0151 Å °-0.1395 Å °-0.028 Å °0.0947 Å °0.2036 Å °-0.1573 Å °0.1139 Å °
Refinement TLS groupSelection details: Chain A and ((residue 4 through 704) or (residue 803))

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