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- PDB-2j63: Crystal structure of AP endonuclease LMAP from Leishmania major -

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Basic information

Entry
Database: PDB / ID: 2j63
TitleCrystal structure of AP endonuclease LMAP from Leishmania major
ComponentsAP-ENDONUCLEASE
KeywordsLYASE / LEISHMANIA / ENDONUCLEASE / BASE EXCISION REPAIR
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / Hydrolases; Acting on ester bonds / lyase activity / DNA repair / DNA binding / metal ion binding / nucleus
Similarity search - Function
AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family ...AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-(apurinic or apyrimidinic site) endonuclease
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsVidal, A.E. / Harkiolaki, M. / Gallego, C. / Castillo-Acosta, V.M. / Ruiz-Perez, L.M. / Wilson, K.S. / Gonzalez-Pacanowska, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure and DNA Repair Activities of the Ap Endonuclease from Leishmania Major.
Authors: Vidal, A.E. / Harkiolaki, M. / Gallego, C. / Castillo-Acosta, V.M. / Ruiz-Perez, L.M. / Wilson, K. / Gonzalez-Pacanowska, D.
History
DepositionSep 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: AP-ENDONUCLEASE
B: AP-ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)101,7342
Polymers101,7342
Non-polymers00
Water2,432135
1
A: AP-ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)50,8671
Polymers50,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: AP-ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)50,8671
Polymers50,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)167.103, 45.009, 115.134
Angle α, β, γ (deg.)90.00, 116.79, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 2 / Auth seq-ID: 90 - 446 / Label seq-ID: 110 - 466

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

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Components

#1: Protein AP-ENDONUCLEASE / APURINIC/APYRIMIDINIC ENDONUCLEASE-REDOX PROTEIN / LMAP


Mass: 50866.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: 252 / Description: ISOLATED IN IRAN AND PROVIDED BY S. MESHNIK / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O15922, DNA-(apurinic or apyrimidinic site) lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPOLY-HISTIDINE N-TERMINUS ADDED FOR PURIFICATION PURPOSES

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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: 1.99 Å3/Da / Density % sol: 38.13 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: HAMPTON SCREEN I CONDITION 42: 20% PEG 8000, 50MM POTASSIUM PHOSPHATE. HANGING DROPS AT 17C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 16, 2001 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→30.6 Å / Num. obs: 27305 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 30 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 37.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DE9

1de9


Resolution: 2.48→105.41 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 20.974 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.59 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1378 5 %RANDOM
Rwork0.2 ---
obs0.203 25926 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.33 Å2
Baniso -1Baniso -2Baniso -3
1--4.73 Å20 Å2-3.27 Å2
2---0.86 Å20 Å2
3---2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.48→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 0 135 5443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9447372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97922.463268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36815878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7831556
X-RAY DIFFRACTIONr_chiral_restr0.110.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024232
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.22505
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23665
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7211.53388
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25225334
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.35332355
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1934.52038
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1328tight positional0.040.05
1321medium positional0.340.5
1328tight thermal0.080.5
1321medium thermal0.572
LS refinement shellResolution: 2.48→2.55 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 83
Rwork0.277 1752
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)
11.63030.31380.50251.044-0.02371.49240.03590.1097-0.14020.01260.0838-0.1266-0.0560.0996-0.1197-0.1070.00150.0482-0.0515-0.0058-0.15459.72650.02643.9108
22.4214-1.51961.26681.9512-0.56521.75840.2587-0.2073-0.5079-0.10220.21270.41870.166-0.2558-0.4714-0.0702-0.0318-0.0521-0.04590.09370.0326-0.479511.882542.9971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A90 - 446
2X-RAY DIFFRACTION2B90 - 446

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