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- PDB-1qtw: HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI DNA REP... -

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Basic information

Entry
Database: PDB / ID: 1qtw
TitleHIGH-RESOLUTION CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI DNA REPAIR ENZYME ENDONUCLEASE IV
ComponentsENDONUCLEASE IV
KeywordsHYDROLASE / DNA REPAIR ENZYME / TIM BARREL / TRINUCLEAR ZN CLUSTER
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding ...deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding / zinc ion binding / cytosol
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.02 Å
AuthorsHosfield, D.J. / Guan, Y. / Haas, B.J. / Cunningham, R.P. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis.
Authors: Hosfield, D.J. / Guan, Y. / Haas, B.J. / Cunningham, R.P. / Tainer, J.A.
History
DepositionJun 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)31,7154
Polymers31,5181
Non-polymers1963
Water6,612367
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.620, 59.560, 50.980
Angle α, β, γ (deg.)90.00, 110.94, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein ENDONUCLEASE IV / E.C.3.1.21.2


Mass: 31518.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6C1, deoxyribonuclease IV
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 400, HEPES, ZNCL2, pH 6.0, VAPOR DIFFUSION, SITTING DROP at 298 K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %mPEG20001reservoir
2100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.02→30 Å / Num. obs: 142898 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.2
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.5 / % possible all: 83.2
Reflection
*PLUS
Highest resolution: 1.02 Å / Lowest resolution: 30 Å / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Num. measured all: 465830
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
SOLVEphasing
SHELXL-97refinement
SCALEPACKdata scaling
RefinementResolution: 1.02→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.148 13710 10 %RANDOM
Rwork0.124 ---
all0.124 136221 --
obs0.124 136221 --
Refinement stepCycle: LAST / Resolution: 1.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 3 367 4768
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d2.5
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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