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Basic information

Entry
Database: PDB / ID: 3ldy
TitleAn extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI
Components
  • DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3')
  • DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3')
  • restriction endonuclease PacI
KeywordsHYDROLASE/DNA / beta-beta-alpha-metal / HNH motif / Zinc clusters / A-A / and T-T base-pairs / HYDROLASE-DNA complex
Function / homologyHerpes Virus-1 - #220 / Herpes Virus-1 / 2-Layer Sandwich / metal ion binding / Alpha Beta / DNA / Restriction endonuclease PacI
Function and homology information
Biological speciesPseudomonas alcaligenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.97 Å
AuthorsShen, B.W. / Heiter, D. / Chan, S.-H. / Xu, S.-Y. / Wilson, G. / Stoddard, B.L.
CitationJournal: Structure / Year: 2010
Title: Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
Authors: Shen, B.W. / Heiter, D.F. / Chan, S.H. / Wang, H. / Xu, S.Y. / Morgan, R.D. / Wilson, G.G. / Stoddard, B.L.
History
DepositionJan 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Jul 17, 2013Group: Refinement description
Revision 1.4Feb 21, 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_ref_seq / 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_asym_id / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: restriction endonuclease PacI
B: DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3')
C: DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4266
Polymers21,2553
Non-polymers1713
Water1,60389
1
A: restriction endonuclease PacI
B: DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3')
C: DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3')
hetero molecules

A: restriction endonuclease PacI
B: DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3')
C: DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,85312
Polymers42,5116
Non-polymers3426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-29 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.908, 115.788, 114.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the operation -X+1, Y, -Z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein restriction endonuclease PacI


Mass: 15784.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas alcaligenes (bacteria) / Gene: pacIR / Plasmid: pVS1 / Production host: Pseudomonas alcaligenes (bacteria) / References: UniProt: D5MNX7*PLUS

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DNA chain , 2 types, 2 molecules BC

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


Mass: 2466.641 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3')


Mass: 3003.993 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 92 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20-24% PEG 3000, 2-5% ethylene glycol, 0.1M sodium citrate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 5.0.110.9774
ROTATING ANODERIGAKU MICROMAX-007 HF21.5418
SYNCHROTRONALS 5.0.231.0719
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDOct 31, 2009mirrors
RIGAKU SATURN 9442CCDJan 1, 2009
ADSC QUANTUM 3153CCDJan 1, 2009mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal, cylindrically bent, Si(220)SINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
3Double-crystal, Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97741
21.54181
31.07191
ReflectionResolution: 1.83→50 Å / Num. obs: 19597 / % possible obs: 87.9 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 26.25 Å2 / Rsym value: 0.066 / Net I/σ(I): 26
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.26 / Num. unique all: 2194 / Rsym value: 0.25 / % possible all: 39.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0104refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.97→28.95 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.79 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R: 0.32 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21725 888 5.1 %RANDOM
Rwork0.1843 ---
all0.186 19083 --
obs0.186 16445 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2--3.35 Å20 Å2
3----3.39 Å2
Refinement stepCycle: LAST / Resolution: 1.97→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 366 3 89 1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211564
X-RAY DIFFRACTIONr_angle_refined_deg1.5422.222191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36523.33357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33315186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.948158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021100
X-RAY DIFFRACTIONr_mcbond_it1.1631.5715
X-RAY DIFFRACTIONr_mcangle_it2.13921137
X-RAY DIFFRACTIONr_scbond_it2.993849
X-RAY DIFFRACTIONr_scangle_it4.4934.51051
X-RAY DIFFRACTIONr_rigid_bond_restr1.67431564
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 51 -
Rwork0.227 953 -
obs--77.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3793-0.221-0.20890.35780.07572.17760.0085-0.12850.01610.03790.037-0.0040.00620.0481-0.04560.01270.0023-0.00310.0979-0.00330.014119.739233.366244.709
23.97291.73113.40412.9019-0.54962.4297-0.2111-0.75890.49240.4353-0.08970.245-0.651-0.57390.30080.27220.03860.03720.185-0.10640.061120.634350.285244.7205
31.4926-0.5942-0.0881-0.0211-0.84792.9266-0.0155-0.39040.24530.09260.0444-0.0532-0.57630.0277-0.02880.13010.00220.00860.0893-0.06920.076422.200947.547843.0979
41.207-2.8272-9.9288-4.7123-8.54143.9678-0.18010.1769-0.5469-0.39580.19110.2422-0.91030.874-0.01090.03060.0094-0.09790.0943-0.0630.119718.952733.190244.6322
50.9432-0.25430.2680.6764-0.90121.6394-0.0194-0.16970.02340.04520.01660.0474-0.0516-0.14170.00280.0521-0.00290.01010.0636-0.02320.043617.801134.23241.1581
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 142
2X-RAY DIFFRACTION2B1 - 8
3X-RAY DIFFRACTION3C9 - 18
4X-RAY DIFFRACTION4A143 - 145
5X-RAY DIFFRACTION5A146 - 233

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