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- PDB-4wa8: Methanopyrus Kandleri FEN-1 nuclease -

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Basic information

Entry
Database: PDB / ID: 4wa8
TitleMethanopyrus Kandleri FEN-1 nuclease
ComponentsFlap endonuclease 1
KeywordsHYDROLASE / DNA nuclease / Nucleotide excision repair
Function / homology
Function and homology information


5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding
Similarity search - Function
Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShah, S. / Dunten, P. / Horton, N.C.
CitationJournal: Proteins / Year: 2015
Title: Structure and specificity of FEN-1 from Methanopyrus kandleri.
Authors: Shah, S. / Dunten, P. / Stiteler, A. / Park, C.K. / Horton, N.C.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flap endonuclease 1
B: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1796
Polymers82,0372
Non-polymers1424
Water1,54986
1
A: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0893
Polymers41,0191
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0893
Polymers41,0191
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.331, 86.193, 147.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 339 / Label seq-ID: 8 - 346

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Flap endonuclease 1 / FEN-1 / Flap structure-specific endonuclease 1


Mass: 41018.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938 / Gene: fen, MK0566 / Plasmid: pMAL_c4X / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TXU4, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, Tris-HCL, sodium chloride, calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→74.43 Å / Num. obs: 35363 / % possible obs: 96.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.2 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RXW

1rxw


Resolution: 2.2→74.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.732 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23134 1758 5 %RANDOM
Rwork0.20011 ---
obs0.20165 33535 96.24 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.506 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2---0.8 Å20 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 2.2→74.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 0 4 86 4842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194832
X-RAY DIFFRACTIONr_bond_other_d0.0030.024704
X-RAY DIFFRACTIONr_angle_refined_deg1.1942.0046531
X-RAY DIFFRACTIONr_angle_other_deg0.879310851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5085585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98324.05242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67715889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4311550
X-RAY DIFFRACTIONr_chiral_restr0.0650.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215366
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021008
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4693.1732361
X-RAY DIFFRACTIONr_mcbond_other1.4693.1722360
X-RAY DIFFRACTIONr_mcangle_it2.3674.7462939
X-RAY DIFFRACTIONr_mcangle_other2.3664.7472940
X-RAY DIFFRACTIONr_scbond_it2.0363.5062471
X-RAY DIFFRACTIONr_scbond_other2.0363.5072472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3295.1453593
X-RAY DIFFRACTIONr_long_range_B_refined5.01525.0785386
X-RAY DIFFRACTIONr_long_range_B_other5.00825.0125364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18860 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 126 -
Rwork0.289 2198 -
obs--88 %
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)
11.1904-0.3442-0.10743.3794-0.93551.713-0.02740.0433-0.2332-0.28830.0348-0.07990.2692-0.0819-0.00740.1666-0.01890.01950.0246-0.03910.10774.873-3.727-12.577
21.40490.94070.32723.589-0.09971.62130.2027-0.2329-0.10180.4355-0.04260.00970.1842-0.1815-0.16010.1858-0.0502-0.01520.0830.03230.02112.0993.87521.338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 339
2X-RAY DIFFRACTION2B1 - 339

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