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- PDB-6c36: Mycobacterium smegmatis flap endonuclease mutant D208N -

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Basic information

Entry
Database: PDB / ID: 6c36
TitleMycobacterium smegmatis flap endonuclease mutant D208N
Components5'-3' exonuclease
KeywordsDNA BINDING PROTEIN / Mycobacterium DNA flab endonuclease FenA
Function / homology
Function and homology information


DNA replication, Okazaki fragment processing / 5'-flap endonuclease activity / exonuclease activity / DNA binding
Similarity search - Function
Flap endonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / 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
: / PHOSPHATE ION / 5'-3' exonuclease
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsShuman, S. / Goldgur, Y. / Carl, A. / Uson, M.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI64693 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)HEI-S10RR029205 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities.
Authors: Uson, M.L. / Carl, A. / Goldgur, Y. / Shuman, S.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-3' exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2175
Polymers33,9571
Non-polymers2604
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-25 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.103, 39.837, 68.313
Angle α, β, γ (deg.)90.00, 108.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5'-3' exonuclease


Mass: 33957.391 Da / Num. of mol.: 1 / Mutation: D208N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_3793 / Production host: Escherichia coli (E. coli) / References: UniProt: I7GAS0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium acetate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 48509 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.068 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.62 / Rpim(I) all: 0.378 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.9→38.211 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.26
RfactorNum. reflection% reflection
Rfree0.2077 3756 7.79 %
Rwork0.1701 --
obs0.173 48502 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→38.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 8 319 2703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062430
X-RAY DIFFRACTIONf_angle_d0.9193324
X-RAY DIFFRACTIONf_dihedral_angle_d2.891479
X-RAY DIFFRACTIONf_chiral_restr0.053386
X-RAY DIFFRACTIONf_plane_restr0.007441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8908-1.91470.3878960.31371291X-RAY DIFFRACTION73
1.9147-1.93990.33441140.31121500X-RAY DIFFRACTION91
1.9399-1.96650.35631530.2671627X-RAY DIFFRACTION93
1.9665-1.99460.33651300.25051621X-RAY DIFFRACTION96
1.9946-2.02430.26841530.22691655X-RAY DIFFRACTION96
2.0243-2.0560.20041180.23051666X-RAY DIFFRACTION97
2.056-2.08970.22351340.21941701X-RAY DIFFRACTION97
2.0897-2.12570.25471850.21261599X-RAY DIFFRACTION97
2.1257-2.16440.23541280.20461661X-RAY DIFFRACTION96
2.1644-2.2060.2191300.19291679X-RAY DIFFRACTION95
2.206-2.2510.24421550.19111670X-RAY DIFFRACTION98
2.251-2.30.1931260.19211661X-RAY DIFFRACTION99
2.3-2.35340.23411510.17971720X-RAY DIFFRACTION99
2.3534-2.41230.20241460.17531710X-RAY DIFFRACTION98
2.4123-2.47750.22911540.1731721X-RAY DIFFRACTION99
2.4775-2.55040.19841390.16721665X-RAY DIFFRACTION98
2.5504-2.63270.21761490.16181724X-RAY DIFFRACTION99
2.6327-2.72680.22281420.16541647X-RAY DIFFRACTION97
2.7268-2.83590.21331270.16851691X-RAY DIFFRACTION96
2.8359-2.96490.20961510.15351658X-RAY DIFFRACTION99
2.9649-3.12120.19691480.16611668X-RAY DIFFRACTION99
3.1212-3.31660.20031450.16121762X-RAY DIFFRACTION99
3.3166-3.57250.16941490.14461688X-RAY DIFFRACTION99
3.5725-3.93170.20171380.12731719X-RAY DIFFRACTION98
3.9317-4.49990.16211510.11831607X-RAY DIFFRACTION96
4.4999-5.66640.14041390.1411732X-RAY DIFFRACTION99
5.6664-38.21910.18291290.16581679X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 31.5734 Å / Origin y: 25.1497 Å / Origin z: 19.033 Å
111213212223313233
T0.1199 Å20.0102 Å2-0.0035 Å2-0.102 Å2-0.0033 Å2--0.1068 Å2
L0.731 °20.1913 °2-0.0606 °2-0.5147 °2-0.1316 °2--0.7425 °2
S-0.0138 Å °0.0676 Å °-0.0246 Å °-0.023 Å °-0.0015 Å °-0.0381 Å °-0.0052 Å °0.0518 Å °0.0156 Å °
Refinement TLS groupSelection details: all

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