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- PDB-2x7w: Crystal structure of Thermotoga maritima endonuclease IV in the p... -

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Basic information

Entry
Database: PDB / ID: 2x7w
TitleCrystal structure of Thermotoga maritima endonuclease IV in the presence of cadmium and zinc
ComponentsPROBABLE ENDONUCLEASE 4
KeywordsHYDROLASE / NUCLEASE / DNA REPAIR / APURINIC-APYRIMIDINIC (AP) METAL-BINDING
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision 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 speciesTHERMOTOGA MARITIMA MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsTomanicek, S.J. / Hughes, R.C. / Ng, J.D. / Coates, L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of the Endonuclease Iv Homologue from Thermotoga Maritima in the Presence of Active-Site Divalent Metal Ions
Authors: Tomanicek, S.J. / Hughes, R.C. / Ng, J.D. / Coates, L.
History
DepositionMar 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE ENDONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9365
Polymers32,4831
Non-polymers4534
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.190, 123.190, 35.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PROBABLE ENDONUCLEASE 4 / ENDONUCLEASE IV / ENDODEOXYRIBONUCLEASE IV


Mass: 32482.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA MSB8 (bacteria) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYJ7, deoxyribonuclease IV
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 46.7 % / Description: NONE
Crystal growpH: 9
Details: 0.1 M SODIUM CHLORIDE, 0.1 M BICINE PH 9.0, 20%(V/V) POLYETHYLENE GLYCOL MONOMETHYL ETHER 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Aug 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→40.32 Å / Num. obs: 12749 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 10.24 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.1
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.2 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QTW

1qtw


Resolution: 2.36→40.32 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 626 4.9 %
Rwork0.156 --
obs0.158 12749 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.68 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 10.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.0314 Å20 Å20 Å2
2---0.0314 Å20 Å2
3---0.0627 Å2
Refinement stepCycle: LAST / Resolution: 2.36→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 14 209 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232348
X-RAY DIFFRACTIONf_angle_d0.7943162
X-RAY DIFFRACTIONf_dihedral_angle_d16.287878
X-RAY DIFFRACTIONf_chiral_restr0.055333
X-RAY DIFFRACTIONf_plane_restr0.003409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3626-2.60040.21241630.15832975X-RAY DIFFRACTION99
2.6004-2.97650.23031450.15953051X-RAY DIFFRACTION100
2.9765-3.74970.1941680.14783034X-RAY DIFFRACTION100
3.7497-40.32920.16311500.15583064X-RAY DIFFRACTION97

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