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- PDB-4cei: Crystal structure of ADPNP-bound AddAB with a forked DNA substrate -

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Basic information

Entry
Database: PDB / ID: 4cei
TitleCrystal structure of ADPNP-bound AddAB with a forked DNA substrate
Components
  • (ATP-DEPENDENT ...) x 2
  • DNA
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / HELICASE-NUCLEASE / BACTERIAL PROTEINS / BINDING SITES / DNA BREAKS / DOUBLE-STRANDED / DNA HELICASES / DNA REPAIR / SINGLE-STRANDED / DNA- BINDING PROTEINS / DEOXYRIBONUCLEASES / EXODEOXYRIBONUCLEASE V / EXODEOXYRIBONUCLEASES / HOMOLOGOUS RECOMBINATION
Function / homology
Function and homology information


DNA helicase complex / 5'-3' exonuclease activity / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity / 3'-5' exonuclease activity / helicase activity / double-strand break repair via homologous recombination / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding ...DNA helicase complex / 5'-3' exonuclease activity / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity / 3'-5' exonuclease activity / helicase activity / double-strand break repair via homologous recombination / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA recombination / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Enzyme I; Chain A, domain 2 - #50 / Helix Hairpins - #1030 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2380 / DNA helicase subunit AddB / DNA helicase subunit AddA / : / ADDB, N-terminal / PCRA; domain 4 / PCRA; domain 4 / Lambda Exonuclease; Chain A - #10 ...Enzyme I; Chain A, domain 2 - #50 / Helix Hairpins - #1030 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2380 / DNA helicase subunit AddB / DNA helicase subunit AddA / : / ADDB, N-terminal / PCRA; domain 4 / PCRA; domain 4 / Lambda Exonuclease; Chain A - #10 / PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / Lambda Exonuclease; Chain A / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / PD-(D/E)XK endonuclease-like domain superfamily / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Restriction endonuclease type II-like / Enzyme I; Chain A, domain 2 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / ATP-dependent helicase/deoxyribonuclease subunit B / ATP-dependent helicase/nuclease subunit A
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKrajewski, W.W. / Wilkinson, M. / Fu, X. / Cronin, N.B. / Wigley, D.
CitationJournal: Nature / Year: 2014
Title: Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites.
Authors: Krajewski, W.W. / Fu, X. / Wilkinson, M. / Cronin, N.B. / Dillingham, M.S. / Wigley, D.B.
History
DepositionNov 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Dec 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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: ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A
B: ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B
X: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,3588
Polymers295,9453
Non-polymers1,4135
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24920 Å2
ΔGint-105.6 kcal/mol
Surface area100710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.944, 151.335, 124.560
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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ATP-DEPENDENT ... , 2 types, 2 molecules AB

#1: Protein ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A / ATP-DEPENDENT HELICAS E-NUCLEASE SUBUNIT A


Mass: 141218.844 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PCOLADUET-1 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 (DE3)
References: UniProt: P23478, Hydrolases; Acting on ester bonds, DNA helicase
#2: Protein ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B / ATP-DEPENDENT HELICAS E-NUCLEASE SUBUNIT B


Mass: 134769.406 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PCOLADUET-1 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 (DE3)
References: UniProt: P23477, Hydrolases; Acting on ester bonds, DNA helicase

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DNA chain , 1 types, 1 molecules X

#3: DNA chain DNA


Mass: 19956.744 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ANNEALED HAIRPIN DUPLEX WITH UNPAIRED SINGLE-STRANDED 3' AND 5' TAILS
Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 13 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP): NON-HYDROLYSABLE ATP ANALOGUE MAGNESIUM ION (MG): ...PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP): NON-HYDROLYSABLE ATP ANALOGUE MAGNESIUM ION (MG): COORDINATED BY PROTEIN, ANP AND WATER MOLECULES

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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: 54 % / Description: NONE
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES PH 7.5, 17.5 % PEG 1500, 0.25M NACL, 0.1M SODIUM FORMATE, 0.1M MGCL2, VAPOR DIFFUSION, HANGING DROP, 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→47.93 Å / Num. obs: 68664 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXPHASER-MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U44

3u44


Resolution: 2.8→29.949 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 3455 5 %
Rwork0.1953 --
obs0.1976 68623 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→29.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18846 757 72 8 19683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420171
X-RAY DIFFRACTIONf_angle_d0.74927365
X-RAY DIFFRACTIONf_dihedral_angle_d17.2737726
X-RAY DIFFRACTIONf_chiral_restr0.0312983
X-RAY DIFFRACTIONf_plane_restr0.0033399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83830.33881300.27862589X-RAY DIFFRACTION99
2.8383-2.87890.34511260.27512618X-RAY DIFFRACTION99
2.8789-2.92180.33191420.26542591X-RAY DIFFRACTION100
2.9218-2.96740.36461270.28512594X-RAY DIFFRACTION100
2.9674-3.0160.38861600.27582584X-RAY DIFFRACTION100
3.016-3.0680.30061320.2612595X-RAY DIFFRACTION100
3.068-3.12370.31341250.25932587X-RAY DIFFRACTION100
3.1237-3.18370.32761480.25132582X-RAY DIFFRACTION100
3.1837-3.24860.30321280.24472597X-RAY DIFFRACTION100
3.2486-3.31920.30411460.23592643X-RAY DIFFRACTION100
3.3192-3.39630.30111340.23112558X-RAY DIFFRACTION100
3.3963-3.48110.2791590.21222593X-RAY DIFFRACTION100
3.4811-3.57510.23791240.20232617X-RAY DIFFRACTION100
3.5751-3.68010.25111440.20292602X-RAY DIFFRACTION100
3.6801-3.79860.24951370.1862622X-RAY DIFFRACTION100
3.7986-3.93410.22531520.18672581X-RAY DIFFRACTION100
3.9341-4.09130.22681360.17432599X-RAY DIFFRACTION100
4.0913-4.2770.22931350.17382632X-RAY DIFFRACTION100
4.277-4.50180.19531230.15612623X-RAY DIFFRACTION100
4.5018-4.78270.18141350.15882645X-RAY DIFFRACTION100
4.7827-5.15030.19631380.1562603X-RAY DIFFRACTION100
5.1503-5.66550.19611490.16622612X-RAY DIFFRACTION100
5.6655-6.4780.19911490.18722608X-RAY DIFFRACTION100
6.478-8.13450.18951370.1742637X-RAY DIFFRACTION100
8.1345-29.95080.17541390.16132656X-RAY DIFFRACTION99

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