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- PDB-3wvg: Time-Resolved Crystal Structure of HindIII with 0sec soaking -

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Basic information

Entry
Database: PDB / ID: 3wvg
TitleTime-Resolved Crystal Structure of HindIII with 0sec 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 / time-resolved / type IIP restriction endonuclease / restriction 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 / Resolution: 2.25 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
G: 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')
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')
E: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
F: 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)169,76023
Polymers169,30012
Non-polymers46011
Water7,728429
1
A: Type-2 restriction enzyme HindIII
B: Type-2 restriction enzyme HindIII
E: DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
F: 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)77,59910
Polymers77,3234
Non-polymers2766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-141 kcal/mol
Surface area25510 Å2
MethodPISA
2
C: Type-2 restriction enzyme HindIII
D: Type-2 restriction enzyme HindIII
G: 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5079
Polymers77,3234
Non-polymers1845
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14670 Å2
ΔGint-142 kcal/mol
Surface area25570 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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10 kcal/mol
Surface area4430 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-10 kcal/mol
Surface area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.656, 140.583, 96.294
Angle α, β, γ (deg.)90.000, 112.100, 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 side
Source: (synth.) synthetic (others)
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-15% PEG 3350, 300mM NaSCN, 10% 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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 93316 / % possible obs: 99.65 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 16.5
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.2 / % possible all: 97.74

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Processing

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

3a4k


Resolution: 2.25→39.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.02 / SU ML: 0.144 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 4714 5.1 %RANDOM
Rwork0.1772 ---
obs0.1797 93315 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.43 Å2 / Biso mean: 38.386 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9808 1944 26 429 12207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01812167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210946
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.80916771
X-RAY DIFFRACTIONr_angle_other_deg0.99325314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24351188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88425.656488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.657152000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6951540
X-RAY DIFFRACTIONr_chiral_restr0.1040.21795
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022760
X-RAY DIFFRACTIONr_mcbond_it3.1233.544764
X-RAY DIFFRACTIONr_mcbond_other3.1223.544763
X-RAY DIFFRACTIONr_mcangle_it4.5545.2965948
LS refinement shellResolution: 2.254→2.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 335 -
Rwork0.273 6353 -
all-6688 -
obs--96.97 %

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