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- PDB-3m7k: Crystal structure of PacI-DNA Enzyme product complex -

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Basic information

Entry
Database: PDB / ID: 3m7k
TitleCrystal structure of PacI-DNA Enzyme product complex
Components
  • DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3')
  • DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3')
  • restriction endonuclease PacI
KeywordsHYDROLASE/DNA / HNH restriction endonuclease / beta-beta-alpha-metal active site / 8 base-pair rare cutter / 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: 1.92 Å
AuthorsShen, B.W. / 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
DepositionMar 16, 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 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_alt_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _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_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*AP*AP*T)-3')
C: DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,06719
Polymers21,2553
Non-polymers81116
Water2,054114
1
A: restriction endonuclease PacI
B: DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3')
C: DNA (5'-D(P*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*AP*AP*T)-3')
C: DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,13438
Polymers42,5116
Non-polymers1,62332
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area14080 Å2
ΔGint-325 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.089, 114.927, 114.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-48-

HOH

DetailsThe second part of the dimeric assembly is generated by the two fold operator -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) / Strain: NEB 585 / Gene: pacIR / Plasmid: pVS1 / Production host: Pseudomonas alcaligenes (bacteria) / Strain (production host): NEB 585 / 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*AP*AP*T)-3')


Mass: 3084.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: top strand product of PacI
#3: DNA chain DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3')


Mass: 2386.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: bottom strand of PacI product

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Non-polymers , 7 types, 130 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22% PEG3K, 2.5% ethylene glycol, 10 mM MgSO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2009 / Details: Double-crystal, Si(111)
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionRedundancy: 7.9 % / Av σ(I) over netI: 36.31 / Number: 151016 / Rmerge(I) obs: 0.053 / Χ2: 1.6 / D res high: 1.91 Å / D res low: 50 Å / Num. obs: 19094 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.115094.110.0484.9047.3
3.274.1199.110.0441.6717.9
2.853.2799.810.0461.4698
2.592.8510010.0541.4328.1
2.412.5910010.0661.2478.2
2.262.4110010.081.0868.3
2.152.2610010.1091.0888.2
2.062.1599.410.1331.1198.2
1.982.069910.1831.0937.8
1.911.9893.810.2261.0856.9
ReflectionResolution: 1.91→50 Å / Num. obs: 19148 / % possible obs: 98.6 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.062 / Χ2: 1.309 / Net I/σ(I): 28.2
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.266 / Num. unique all: 1761 / Χ2: 1.046 / % possible all: 92.4

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Phasing

PhasingMethod: MIR
Phasing dmFOM : 0.81 / FOM acentric: 0.8 / FOM centric: 0.82 / Reflection: 4866 / Reflection acentric: 4077 / Reflection centric: 789
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-19.6030.910.920.9123414292
5.4-8.60.890.90.88688533155
4.3-5.40.870.880.81837692145
3.8-4.30.850.860.8830711119
3.2-3.80.780.770.8114431257186
3-3.20.650.650.6483474292
Phasing MIR der
IDDer set-ID
11
21
31
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1148.689Pt0.33620.39020.06560.5189
1260Pt0.04810.33210.13390.6061
1353.9088Pt0.88630.33310.15110.2962
2160Pt0.34850.38510.060.3802
221Pt0.66480.33420.14920.1256
231Pt0.81790.33020.15890.0211
3135.2596Pt0.35870.39270.05370.3106
4136.1292Hg0.86680.15110.00950.3521
515W0.95120.16320.00750.0895

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.92→20.26 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.201 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.867 / SU B: 7 / SU ML: 0.091 / SU R Cruickshank DPI: 0.249 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.201 976 5.2 %RANDOM
Rwork0.172 ---
obs0.173 18941 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 151.19 Å2 / Biso mean: 45.109 Å2 / Biso min: 18.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å2-0 Å20 Å2
2--3.55 Å2-0 Å2
3----4.7 Å2
Refinement stepCycle: LAST / Resolution: 1.92→20.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 367 27 114 1610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211608
X-RAY DIFFRACTIONr_angle_refined_deg1.3052.2222259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1995159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.723.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26415195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.405159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021133
X-RAY DIFFRACTIONr_mcbond_it1.31.5730
X-RAY DIFFRACTIONr_mcangle_it2.36521167
X-RAY DIFFRACTIONr_scbond_it2.7673878
X-RAY DIFFRACTIONr_scangle_it4.1724.51084
X-RAY DIFFRACTIONr_rigid_bond_restr1.54431608
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 70 -
Rwork0.217 1251 -
all-1321 -
obs--95.24 %
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)
10.0839-0.0766-0.07120.5359-0.10271.29850.011-0.0338-0.0030.08310.0296-0.01130.01730.0182-0.04060.0231-0.005-0.00560.0260.00160.002519.769132.849744.5516
20.5695-0.0365-0.01250.90790.96911.90790.0251-0.01080.11210.0916-0.02810.025-0.1036-0.03890.0030.0721-0.00790.02110.0101-0.01010.030221.187347.261440.622
30.39750.0476-0.27850.1889-0.17152.00670.0023-0.13120.01730.0151-0.0131-0.0322-0.22190.26220.01080.05870.01230.01250.12250.03360.087824.237149.031645.5685
40.10460.0495-0.18531.15840.04740.94930.04550.0442-0.0656-0.033-0.0780.0359-0.07110.03740.03260.05260.0216-0.03050.1203-0.07610.112521.191632.435741.9831
5356.6372-414.3076-116.4308481.3037135.258438.0111.44891.21760.2026-1.6642-1.4002-0.2358-0.4657-0.3963-0.04870.1829-0.05270.10520.23680.0410.16364.8128.477231.1667
60.830.1752-0.07620.41740.14581.57240.018-0.0714-0.0210.0922-0.0105-0.0359-0.00080.0562-0.00760.0254-0.0025-0.00530.03160.00170.023320.957133.684541.3719
77.117-7.77313.40938.4918-3.72431.63350.32150.0009-0.4596-0.4219-0.05810.50410.17960.0074-0.26340.55430.11230.090.1742-0.07260.132418.609422.697148.7351
800000000000000-00.0383000.038300.0383000
900000000000000-00.0383000.038300.0383000
1000000000000000-00.0383000.038300.0383000
1100000000000000-00.0383000.038300.0383000
1200000000000000-00.0383000.038300.0383000
1300000000000000-00.0383000.038300.0383000
1400000000000000-00.0383000.038300.0383000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 142
2X-RAY DIFFRACTION2B1 - 10
3X-RAY DIFFRACTION3C11 - 18
4X-RAY DIFFRACTION4A1 - 153
5X-RAY DIFFRACTION5A1 - 154
6X-RAY DIFFRACTION6A1 - 248
7X-RAY DIFFRACTION7A1 - 156
8X-RAY DIFFRACTION8A1 - 142
9X-RAY DIFFRACTION9B1 - 10
10X-RAY DIFFRACTION10C11 - 18
11X-RAY DIFFRACTION11A1 - 153
12X-RAY DIFFRACTION12A1 - 154
13X-RAY DIFFRACTION13A1 - 248
14X-RAY DIFFRACTION14A1 - 156

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