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- PDB-6ukh: HhaI endonuclease in Complex with DNA in space group P41212 (pH 6.0) -

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Basic information

Entry
Database: PDB / ID: 6ukh
TitleHhaI endonuclease in Complex with DNA in space group P41212 (pH 6.0)
Components
  • DNA (5'-D(*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3')
  • DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*G)-3')
  • HhaI Restriction Endonuclease
KeywordsHYDROLASE/DNA / restriction / modification / protein-DNA complex / iodine phasing / HYDROLASE-DNA complex
Function / homologyDNA / DNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesHaemophilus parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom.
Authors: Horton, J.R. / Yang, J. / Zhang, X. / Petronzio, T. / Fomenkov, A. / Wilson, G.G. / Roberts, R.J. / Cheng, X.
History
DepositionOct 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 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
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: HhaI Restriction Endonuclease
A: DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6195
Polymers38,5393
Non-polymers802
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-56 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.257, 67.257, 171.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein HhaI Restriction Endonuclease


Mass: 29977.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parahaemolyticus (bacteria)
Gene: HMPREF1050_0931 / Production host: Escherichia coli (E. coli) / References: UniProt: I3DBY6, Hydrolases
#2: DNA chain DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*G)-3')


Mass: 4302.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus (bacteria)
#3: DNA chain DNA (5'-D(*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3')


Mass: 4258.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus (bacteria)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% v/v 2-propanol, 0.1 M MES/sodium hydroxide, pH 6.0, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.82→33 Å / Num. obs: 17964 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 74.21 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.039 / Net I/σ(I): 16.8
Reflection shellResolution: 2.82→2.93 Å / Redundancy: 11 % / Rmerge(I) obs: 1.685 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1808 / CC1/2: 0.741 / Rpim(I) all: 0.529

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6UKE

6uke


Resolution: 2.82→33 Å / SU ML: 0.4432 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.3289
RfactorNum. reflection% reflection
Rfree0.2519 882 4.92 %
Rwork0.2051 --
obs0.2075 17912 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 84.21 Å2
Refinement stepCycle: LAST / Resolution: 2.82→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 527 2 11 2532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362648
X-RAY DIFFRACTIONf_angle_d0.63813701
X-RAY DIFFRACTIONf_chiral_restr0.0438407
X-RAY DIFFRACTIONf_plane_restr0.004385
X-RAY DIFFRACTIONf_dihedral_angle_d22.77972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-30.43381420.33992786X-RAY DIFFRACTION97.67
3-3.230.28721500.25222840X-RAY DIFFRACTION100
3.23-3.560.2621420.21862870X-RAY DIFFRACTION99.97
3.56-4.070.26321500.19892839X-RAY DIFFRACTION100
4.07-5.130.21951460.17472844X-RAY DIFFRACTION99.97
5.13-330.23281520.1942851X-RAY DIFFRACTION100
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)
17.51017006856-5.22236233237-5.616359674078.665368955695.718111237279.246732244110.7202163023440.5304831628160.442471866202-0.437048573878-0.2660703540950.574881884033-1.48992880232-0.128206438671-0.4967818566840.6500522363010.0224601536441-0.06061080869350.4217497771880.06055903111160.899353065544-20.119795550646.2940436103-16.1008703066
28.367690048229.80693329991-3.040860411882.16813426178-2.082380106189.16643650449-1.00979607846-0.789772121117-1.08954123858-0.3174306414790.586488269894-1.429358847850.09823542087221.450926655070.3453386424040.8291519737790.214009312780.1823956910220.618777221249-0.07244546461821.09435616053-19.238743051942.1730897141-6.67838292486
32.04631860373-3.87093771616-0.1701097406835.207294946862.624350284865.88202060615-0.09469051166380.0403128154034-0.2674275060660.02687967095810.1396986557580.627107833875-0.177589736294-0.740914502743-0.06055189932940.338986666624-0.0655423341870.1199324494560.4936393302170.04358767007760.585801585201-23.445636754837.6117154798-11.3287471329
42.673580948734.976649008053.079107446987.68640347549-2.230545077629.001925948370.437483987225-0.623763580975-1.581099652772.19251342258-0.0805873609622-0.006318533657060.8204991161280.172827385273-0.3940189802320.808423715427-0.1690145099940.02613253029150.586377981860.1029741301290.821870695624-12.428606815212.8121771667-8.94795623769
52.27152392129-8.10083651059-0.1414084802756.57727082426-0.1630820091167.9214643309-0.0199705079265-0.406141839953-1.73685986819-0.126980393564-0.256192760621.145610719632.05489808610.0649181934278-0.1230749241740.718786571006-0.1400873806150.09193520712970.535814868108-0.1101304664390.965263826069-18.11351199149.38965760501-16.1990822267
64.222190961440.4292394701650.2217110047444.709901626780.5993763103422.36033623445-0.1810336517930.0960039596651-0.1245697777780.01874210635790.1388442862090.5272709500570.02889970230940.0462659187155-0.001175547574370.477062567597-0.1300082160080.1045594295710.483202841414-0.08047069815060.42474204702-19.289534793726.6847745592-16.9424505333
77.38063581675-0.746707198896-2.231410603520.6234759645341.308832706817.764311390260.850175560726-0.303786993358-0.185815332707-0.1396428957920.633708181435-1.45763064412-1.04317452511.91944673163-1.488186962030.988567319798-0.3784710925540.01411877073381.44330942052-0.5098817586121.1030919630315.747466377139.2470468852-10.4569157188
89.795414082337.76771969533-5.667533518592.39930524222-5.742829248215.35251619035-0.02296969691740.0548290038823-0.8248649867260.4485802198110.111694990975-1.18593854815-0.3721125856150.2316590977810.04298287067820.580812235895-0.0867222123366-0.08905105588080.728926310535-0.176711052120.7050037351157.1065895970133.1740611523-11.9921329631
97.81825199217-4.6017278562-2.363275900866.842942090941.05213185060.4976769184430.474204360560.830989962905-0.575698328899-1.33328642363-0.4583137986860.5300647048980.07446639303480.0506060418346-0.219181896770.615619164093-0.1402471995680.004988322552110.486114156166-0.1167625998690.605798541348-21.133665152327.5575794419-22.925160636
102.460192914142.303147360872.714999607087.503525244355.465224426576.8262572118-0.447527181584-0.3564602674280.467320871472-0.1393731596950.8878928179021.184664015680.219320346514-0.813873322696-0.3057485554080.6423336369750.19907745882-0.08699020022720.7267066937920.1002574399721.53454754232-36.950854689540.9017154997-16.8955542754
110.9792519355580.832733232090.7798166731729.5345238482.809049095092.394739736920.329295441170.628051713077-0.01776055100241.04644695968-0.379023861066-1.49533755297-0.4648254119322.178192654090.1594721253690.713699190985-0.117649452693-0.09581411999221.150560843460.08994042449640.595741305739-4.5582525048629.0695832757-11.2626953142
126.28893948507-0.427357478172-3.879181117576.65028684019-1.774128072089.781988199950.425699393194-1.10567829167-0.4069510929490.5824058648070.216355412304-0.4364391343131.01793007998-0.61136974008-0.6637174425160.609323464174-0.225351768405-0.05463689670080.8564469714210.1468866764910.50127592028-5.0092734849127.7602965371-11.1603555008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'X' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'X' and (resid 19 through 34 )
3X-RAY DIFFRACTION3chain 'X' and (resid 35 through 55 )
4X-RAY DIFFRACTION4chain 'X' and (resid 56 through 79 )
5X-RAY DIFFRACTION5chain 'X' and (resid 80 through 96 )
6X-RAY DIFFRACTION6chain 'X' and (resid 97 through 165 )
7X-RAY DIFFRACTION7chain 'X' and (resid 166 through 198 )
8X-RAY DIFFRACTION8chain 'X' and (resid 199 through 227 )
9X-RAY DIFFRACTION9chain 'X' and (resid 228 through 241 )
10X-RAY DIFFRACTION10chain 'X' and (resid 242 through 258 )
11X-RAY DIFFRACTION11chain 'A' and (resid 1 through 13 )
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 14 )

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