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- PDB-3bam: RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE ION... -

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Basic information

Entry
Database: PDB / ID: 3bam
TitleRESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)
Components
  • DNA (5'-D(*TP*AP*TP*G)-3')
  • DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
  • DNA (5'-D(P*GP*AP*TP*CP*CP*AP*TP*A)-3')
  • PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)
KeywordsHYDROLASE/DNA / HYDROLASE / PHOSPHODIESTERASE / COMPLEX (ENDONUCLEASE-DNA) / NUCLEASE / PROTEIN/DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding
Similarity search - Function
Restriction endonuclease, type II, BamHI / Restriction endonuclease BamHI / Restriction endonuclease, type II, BamHI/BglIII/BstY / Restriction Endonuclease - #20 / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Type II restriction enzyme BamHI
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsViadiu, H. / Aggarwal, A.K.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: The role of metals in catalysis by the restriction endonuclease BamHI.
Authors: Viadiu, H. / Aggarwal, A.K.
#1: Journal: Science / Year: 1995
Title: Structure of Bam Hi Endonuclease Bound to DNA: Partial Folding and Unfolding on DNA Binding
Authors: Newman, M. / Strzelecka, T. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionAug 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_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_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_asym_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
C: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
D: DNA (5'-D(*TP*AP*TP*G)-3')
E: DNA (5'-D(P*GP*AP*TP*CP*CP*AP*TP*A)-3')
A: PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)
B: PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5927
Polymers56,4825
Non-polymers1102
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.400, 79.600, 67.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO BAMHI MONOMERS (CHAINS A AND B) BOUND TO A PALINDROMIC 12 BASE PAIR DNA COMPLEX.

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Components

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DNA chain , 3 types, 3 molecules CDE

#1: DNA chain DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')


Mass: 3661.416 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*TP*G)-3')


Mass: 1205.841 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*GP*AP*TP*CP*CP*AP*TP*A)-3')


Mass: 2410.618 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#4: Protein PROTEIN (RESTRICTION ENDONUCLEASE BAMHI) / E.C.3.1.21.4 / R. BAMHI


Mass: 24602.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CRYSTAL GROWN IN THE PRESENCE OF MANGANESE IONS. / Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P23940, type II site-specific deoxyribonuclease

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Non-polymers , 2 types, 354 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE C-TERMINALS ARE ASYMMETRICALLY POSITIONED BETWEEN THE TWO MONOMERS MAKING UP THE COMPLEX.

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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: 2.52 Å3/Da / Density % sol: 51.22 % / Description: CRYSTAL WAS ISOMORPHOUS TO 1BHM.
Crystal growpH: 5.3
Details: pH 5.3 CATALYSIS OCCURRED IN THE CRYSTAL AFTER SOAKING MANGANESE ION. THE ACTIVE SITE OF THE R SUBUNIT CLEAVED THE ORIGINAL D STRAND IN TWO (D AND E) RESULTING IN A POST-REACTIVE COMPLEX.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120-25 mg/mlprotein1drop
20.5 M1dropKCl
320 mMpotassium phosphate1droppH6.9
41 mMdithiothreitol1drop
510 %glycerol1drop
610 mg/mlDNA1drop
712-14 %PEG80001drop
80.1 MMES1droppH5.3
912-14 %PEG80001reservoir
100.15 M1reservoirKCl
110.1 MMES1reservoirpH5.3
125 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.908
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 40212 / % possible obs: 72 % / Observed criterion σ(I): 0 / Redundancy: 2.77 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.09
Reflection
*PLUS
Num. measured all: 111430
Reflection shell
*PLUS
% possible obs: 45.6 % / Rmerge(I) obs: 0.318

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BHM

1bhm


Resolution: 1.8→8 Å / Rfactor Rfree error: 0 / Cross valid method: R-FREE / σ(F): 2
Details: THE MANGANESE METALS WERE BOUND ONLY IN ONE ACTIVE SITE OF THE DIMER (THE R-SUBUNIT).
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1171 3 %RANDOM
Rwork0.226 ---
obs0.226 33484 72 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 466 2 352 4177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAMCSDX_MOD.PRO
X-RAY DIFFRACTION2PARAM_NDBX_HIGH.DNA
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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