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- PDB-3wvi: Time-Resolved Crystal Structure of HindIII with 40 sec soaking -

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Basic information

Entry
Database: PDB / ID: 3wvi
TitleTime-Resolved Crystal Structure of HindIII with 40 sec soaking
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
  • Type-2 restriction enzyme HindIII
KeywordsHYDROLASE/DNA / FREEZE-TRAP / type IIP restriction endonuclease / endonuclease / hydrolase / nuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system
Similarity search - Function
Type II restriction endonuclease, HindIII / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1510 / Restriction endonuclease, type II, HindIII / Restriction endonuclease, type II, HindIII superfamily / HindIII restriction endonuclease / Restriction Endonuclease / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Type II restriction enzyme HindIII
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsKawamura, T. / Kobayashi, T. / Watanabe, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
Authors: Kawamura, T. / Kobayashi, T. / Watanabe, N.
History
DepositionMay 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_asym_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_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: Type-2 restriction enzyme HindIII
B: Type-2 restriction enzyme HindIII
C: Type-2 restriction enzyme HindIII
D: Type-2 restriction enzyme HindIII
F: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
H: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
G: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
K: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
L: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
I: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
J: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,10824
Polymers169,30012
Non-polymers80812
Water6,810378
1
A: Type-2 restriction enzyme HindIII
B: Type-2 restriction enzyme HindIII
F: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,72710
Polymers77,3234
Non-polymers4046
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14930 Å2
ΔGint-114 kcal/mol
Surface area25570 Å2
MethodPISA
2
C: Type-2 restriction enzyme HindIII
D: Type-2 restriction enzyme HindIII
H: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
G: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,72710
Polymers77,3234
Non-polymers4046
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15050 Å2
ΔGint-111 kcal/mol
Surface area25350 Å2
MethodPISA
3
K: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
L: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-9 kcal/mol
Surface area4440 Å2
MethodPISA
4
I: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
J: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-10 kcal/mol
Surface area4420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.610, 143.236, 94.363
Angle α, β, γ (deg.)90.000, 113.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type-2 restriction enzyme HindIII / R.HindIII / Endonuclease HindIII / Type II restriction enzyme HindIII


Mass: 34998.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: hindIIIR, HI_1393 / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P43870, type II site-specific deoxyribonuclease
#2: DNA chain
DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')


Mass: 3663.392 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: This DNA sequence synthesized chemically contains cognate HindIIIR recognition sequence and elongated scaffolds on both sides
Source: (synth.) synthetic (others)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-15% PEG 3350, 300mM NaSCN, 10% v/v Glycerol, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 8, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 64086 / % possible obs: 99.71 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.78 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 14.2
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A4K

3a4k


Resolution: 2.55→32.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.946 / SU ML: 0.189 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.448 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 3249 5.1 %RANDOM
Rwork0.1729 ---
obs0.1759 64085 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.25 Å2 / Biso mean: 31.379 Å2 / Biso min: 6.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.55→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9808 1944 32 378 12162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01812179
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210959
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.8116787
X-RAY DIFFRACTIONr_angle_other_deg1.005325345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13251190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.10525.665489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51152002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5361540
X-RAY DIFFRACTIONr_chiral_restr0.090.21797
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022763
X-RAY DIFFRACTIONr_mcbond_it2.1552.9914766
X-RAY DIFFRACTIONr_mcbond_other2.1542.994765
X-RAY DIFFRACTIONr_mcangle_it3.3954.4815951
LS refinement shellResolution: 2.545→2.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 240 -
Rwork0.267 4315 -
all-4555 -
obs--96.16 %

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