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- PDB-1xp3: Crystal Structure of Endonuclease IV (BA4508) from Bacillus anthr... -

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Basic information

Entry
Database: PDB / ID: 1xp3
TitleCrystal Structure of Endonuclease IV (BA4508) from Bacillus anthracis at 2.57A Resolution.
Componentsendonuclease IV
KeywordsHYDROLASE / endonuclease IV / nfo / DNA replication / DNA recombination / DNA repair / SPINE / Structural Genomics / Structural Proteomics in Europe
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / DNA repair / DNA binding / zinc ion binding
Similarity search - Function
AP endonucleases family 2 signature 1. / AP endonucleases family 2 signature 2. / AP endonuclease 2, zinc binding site / AP endonucleases family 2 signature 3. / AP endonucleases family 2 profile. / AP endonuclease 2 / AP endonuclease family 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel ...AP endonucleases family 2 signature 1. / AP endonucleases family 2 signature 2. / AP endonuclease 2, zinc binding site / AP endonucleases family 2 signature 3. / AP endonucleases family 2 profile. / AP endonuclease 2 / AP endonuclease family 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Probable endonuclease 4
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsFogg, M.J. / Levdikov, V.M. / Blagova, E.V. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S. / Structural Proteomics in Europe (SPINE)
CitationJournal: To be Published
Title: Crystal Structure of Endonuclease IV (BA4508) from Bacillus anthracis at 2.57A Resolution.
Authors: Fogg, M.J. / Levdikov, V.M. / Blagova, E.V. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionOct 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: endonuclease IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4206
Polymers34,0321
Non-polymers3885
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.886, 55.390, 64.972
Angle α, β, γ (deg.)90.00, 89.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein endonuclease IV / Endodeoxyribonuclease IV


Mass: 34031.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: nfo / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q81LV1, deoxyribonuclease IV
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.7 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2004 / Details: Rh coated Si mirror
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. all: 10633 / Num. obs: 10633 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 14
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4 / Num. unique all: 964 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QTW

1qtw


Resolution: 2.57→22.83 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.933 / SU B: 16.749 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.917 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22808 532 4.8 %RANDOM
Rwork0.15117 ---
all0.15478 10606 --
obs0.15478 10606 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.983 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.12 Å2
2--0.2 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.57→22.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 13 210 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222362
X-RAY DIFFRACTIONr_bond_other_d0.0030.022148
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9623188
X-RAY DIFFRACTIONr_angle_other_deg0.93935035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2825298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33625.327107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.146159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined0.2220.2659
X-RAY DIFFRACTIONr_nbd_other0.1980.22379
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21133
X-RAY DIFFRACTIONr_nbtor_other0.0920.21371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6561.51893
X-RAY DIFFRACTIONr_mcbond_other0.1131.5615
X-RAY DIFFRACTIONr_mcangle_it0.83722370
X-RAY DIFFRACTIONr_scbond_it1.46831001
X-RAY DIFFRACTIONr_scangle_it2.3084.5817
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 36 -
Rwork0.232 754 -
obs-532 100 %
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)
15.3681-0.0411.47020.61261.6034.65830.40520.4394-0.4804-0.2391-0.161-0.05210.62560.086-0.24420.19120.0208-0.02430.0308-0.05050.0143-33.906-11.0126.856
22.5709-0.99641.2232.3056-1.29214.07640.20510.4771-0.0351-0.3044-0.2222-0.28820.34060.46270.0172-0.02190.04460.0592-0.08980.007-0.0168-18.366-6.4719.252
33.49730.0722-0.14811.40440.3221.95490.11950.18640.3091-0.1639-0.076-0.0724-0.141-0.1176-0.0434-0.08010.00870.0486-0.16830.0342-0.1034-33.8575.15722.683
46.5732-0.83711.12187.04171.74878.453-0.2362-0.193-0.59240.01130.35030.72210.8462-1.1445-0.11410.0349-0.1062-0.02890.21250.0059-0.0432-52.534-6.57317.209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 73
2X-RAY DIFFRACTION2A74 - 146
3X-RAY DIFFRACTION3A147 - 261
4X-RAY DIFFRACTION4A262 - 298

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