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- PDB-1sa3: An asymmetric complex of restriction endonuclease MspI on its pal... -

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Basic information

Entry
Database: PDB / ID: 1sa3
TitleAn asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site
Components
  • 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
  • Type II restriction enzyme MspI
Keywordshydrolase/DNA / PROTEIN-DNA COMPLEX / hydrolase-DNA COMPLEX
Function / homologyRestriction endonuclease, type II, MspI / Restriction endonuclease MspI / type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / Restriction endonuclease type II-like / DNA binding / DNA / Type II restriction enzyme MspI
Function and homology information
Biological speciesMoraxella sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / combination of MAD, MIRAS / Resolution: 1.95 Å
AuthorsXu, Q.S. / Kucera, R.B. / Roberts, R.J. / Guo, H.C.
CitationJournal: STRUCTURE / Year: 2004
Title: An Asymmetric Complex of Restriction Endonuclease MspI on Its Palindromic DNA Recognition Site.
Authors: Xu, Q.S. / Kucera, R.B. / Roberts, R.J. / Guo, H.C.
History
DepositionFeb 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_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_asym_id / _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_asym_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: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
D: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
E: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
F: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
A: Type II restriction enzyme MspI
B: Type II restriction enzyme MspI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9868
Polymers71,9406
Non-polymers462
Water5,963331
1
C: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
D: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
A: Type II restriction enzyme MspI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9934
Polymers35,9703
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
F: 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
B: Type II restriction enzyme MspI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9934
Polymers35,9703
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.193, 131.601, 59.318
Angle α, β, γ (deg.)90.00, 109.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'


Mass: 3046.980 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein Type II restriction enzyme MspI / Endonuclease MspI / R.MspI


Mass: 29876.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella sp. (bacteria) / Gene: MSPIR / Plasmid: pCAD39 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2502
References: UniProt: P11405, type II site-specific deoxyribonuclease
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.67 Å3/Da / Density % sol: 53.58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: MES, ammonium sulfate, calcium chloride, PEG 8000, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9207 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: May 20, 2000
Details: double-crystal monochromator Si(111), beam focused by a toroidal mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double-crystal monochromator Si(111)SINGLE WAVELENGTHMx-ray1
2Mirror + Ni FILTERSINGLE WAVELENGTHMx-ray1
3double-crystal monochromator Si(111)MADMx-ray1
Radiation wavelengthWavelength: 0.9207 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. all: 53664 / Num. obs: 52241 / % possible obs: 97.4 % / Observed criterion σ(I): -2.5 / Redundancy: 2.93 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.043 / Net I/σ(I): 24.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.89 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2671 / Rsym value: 0.275 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: combination of MAD, MIRAS / Resolution: 1.95→42.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2004540.11 / Data cutoff high rms absF: 2004540.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 5172 10.1 %RANDOM
Rwork0.223 ---
all0.225 51260 --
obs0.225 51260 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5597 Å2 / ksol: 0.327728 e/Å3
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å22.02 Å2
2--5.24 Å20 Å2
3----3.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 726 2 331 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.692
X-RAY DIFFRACTIONc_scangle_it3.842.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 869 10 %
Rwork0.26 7801 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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