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- PDB-6uki: HhaI endonuclease in Complex with DNA in space group P212121 (pH 6.0) -

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Basic information

Entry
Database: PDB / ID: 6uki
TitleHhaI endonuclease in Complex with DNA in space group P212121 (pH 6.0)
Components
  • DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*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: 2.7 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.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

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


Theoretical massNumber of molelcules
Total (without water)77,30011
Polymers77,0776
Non-polymers2225
Water41423
1
X: HhaI Restriction Endonuclease
A: DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*GP*A)-3')
B: DNA (5'-D(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6816
Polymers38,5393
Non-polymers1423
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-52 kcal/mol
Surface area15680 Å2
MethodPISA
2
Y: HhaI Restriction Endonuclease
D: DNA (5'-D(*CP*TP*GP*TP*TP*GP*CP*GP*CP*TP*TP*GP*GP*A)-3')
E: DNA (5'-D(*TP*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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-50 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.411, 94.998, 97.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules XY

#1: Protein HhaI Restriction Endonuclease


Mass: 29977.062 Da / Num. of mol.: 2
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

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DNA chain , 2 types, 4 molecules ADBE

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


Mass: 4302.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus (bacteria)
#3: DNA chain DNA (5'-D(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*AP*G)-3')


Mass: 4258.796 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus (bacteria)

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Non-polymers , 3 types, 28 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
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 12, 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: 2.69→33.98 Å / Num. obs: 45835 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 61.51 Å2 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.078 / Net I/σ(I): 11.2
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.749 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4545 / CC1/2: 0.505 / Rpim(I) all: 0.757 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SERGUI1.15.2_3472data 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: 2.7→33.97 Å / SU ML: 0.3197 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.4104
RfactorNum. reflection% reflection
Rfree0.2241 2301 5.03 %
Rwork0.1796 --
obs0.1818 45723 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 76.25 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 1136 8 23 5256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00455472
X-RAY DIFFRACTIONf_angle_d0.68857629
X-RAY DIFFRACTIONf_chiral_restr0.0463830
X-RAY DIFFRACTIONf_plane_restr0.004778
X-RAY DIFFRACTIONf_dihedral_angle_d14.20073028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.3481890.31821913X-RAY DIFFRACTION68.82
2.75-2.820.38091430.29112764X-RAY DIFFRACTION98.61
2.82-2.890.31221430.27192805X-RAY DIFFRACTION99.49
2.89-2.970.26591360.26162819X-RAY DIFFRACTION99.56
2.97-3.050.32711500.25932707X-RAY DIFFRACTION99.62
3.05-3.150.29841420.22562800X-RAY DIFFRACTION99.32
3.15-3.260.26411500.19252763X-RAY DIFFRACTION99.69
3.26-3.40.22261510.17392777X-RAY DIFFRACTION99.15
3.4-3.550.24041350.17682732X-RAY DIFFRACTION99.14
3.55-3.740.22471480.17722768X-RAY DIFFRACTION99.69
3.74-3.970.21831510.16462773X-RAY DIFFRACTION99.39
3.97-4.280.16421560.14962781X-RAY DIFFRACTION99.9
4.28-4.710.16811580.1372766X-RAY DIFFRACTION99.69
4.71-5.380.21991600.14682757X-RAY DIFFRACTION99.69
5.38-6.780.23631470.17342782X-RAY DIFFRACTION99.59
6.78-33.970.21420.17812715X-RAY DIFFRACTION97.41
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)
18.09814844071-0.558333376645-1.038979918035.12599485716-1.498350654326.62525839980.353347510628-0.4433661900360.6277971060830.229356020480.0106289986564-0.195487965805-0.3992504807090.248000190566-0.5773219113390.337212458075-0.0369353078867-0.0001809069483440.288201919383-0.02359506411850.44001217343312.1358076774-3.723655153-34.2855581768
22.336910815640.317385310244-1.380009083513.53112336539-2.120579583267.4146525358-0.319390555844-0.385245946374-0.409864222071-0.20743894892-0.243612984588-0.174654390041.230693731890.4281479098250.44728648770.3832331308570.07964176564640.1162326496140.3312438402320.05952029305790.48352107826312.4552761055-24.1401822179-27.7175701488
33.77473431702-0.871612882707-2.812953315.479060137861.753107837587.48311714499-0.0148602137988-0.5278233104890.4220232530021.19057124865-0.2742281167260.07616362711190.04869217224760.05927595876080.2218970392950.265036948027-0.0790356659177-0.05249406822780.6091394176680.01481715457670.4114089617158.31973088368-9.90431539779-9.84459412633
45.72854302252-2.83562641988-1.782056107524.996517540916.530084823889.556294825670.132088735591-0.7021202861390.969264994640.2108255647110.00928446536937-0.104910315001-1.231321968660.453653772529-0.1656545815730.641192625967-0.04804272592070.03956345339560.711294104232-0.09889175500730.587911366997.64340360020.326602991696-4.83501604284
57.22807487318-1.75163662978-2.642125308164.34844296751-1.198744421617.45547816930.03377301676150.6699513786150.0212199180041-1.09328332048-0.701205022206-0.890161127750.5202251135421.077242884150.5765846766040.5093644850430.04219457667070.1807004469240.3464445908530.0234028144970.52401167779820.3616126155-16.2683527723-40.4255891449
63.62533347251-0.2102206236752.212128218795.69892700691-0.7504942060282.95749397262-0.556915784808-1.984959454470.2539345623760.5279214162550.0251121364956-0.0430864261982-0.3003328384570.6867588665890.3162365308610.335265808935-0.0205491309272-0.08421713100040.992288770165-0.07097681338770.5294754357869.77762208387-12.3232522417-15.3294869942
73.164674947310.439677047904-1.696110157336.844558280791.037040806565.40127241216-0.7814117303650.00105748852833-0.6669122436360.2881148639030.136279780161-0.100543113959-0.1058215668710.5010414260930.3187028130510.297716821205-0.0614665878190.04267345922950.812976750310.02680012725290.62202700119.56682392396-13.7611139478-16.0460823889
84.27661397278-2.292219613373.505518603484.82070945071-4.752632399818.78647612104-0.0613139705499-0.5406815654940.1714526710540.5596283428530.08481746666030.100769279761-0.675186456911-0.485155178224-0.03757039132980.3137301889890.0277427738367-0.01679224243210.567292938826-0.1139741549680.440219758946-11.2132263736-4.34089690074-43.8334900141
92.706305897710.1962435529541.540656958043.23159893081-1.096094388255.8155884982-0.08805219837770.3460247245070.202483510869-0.5640568624770.363819749241-0.2955765098840.3983157050180.2070888978-0.3385315734190.308501490973-0.09396699407580.01125580355050.434679068537-0.09596869903880.47302683515-10.5622064372-6.02839641993-64.3963377185
108.959474904141.22431528248-0.898121558783.255863498154.186914089477.3610170747-0.1013872379990.04795757325751.91555770501-0.9124961044950.306368527554-0.388469896654-1.66310667655-0.289471793281-0.2684266230730.911599754685-0.0438291608253-0.0963169036160.5639215403930.1020639305231.04757464733-10.410980633122.6814550375-59.1183418693
112.972864402490.9660900407691.16385085123.40841700394-2.322027229535.61048289870.3238565266-0.271339738318-0.5555445483990.01187211738450.5514959533870.6169930296010.470265834269-1.08731113676-0.8312183235190.366228326743-0.104023047647-0.08478484711280.5629476386490.03640924609060.539949991634-18.0719852611-15.6213748894-47.3122519153
120.431478904732-0.1987351319141.615025002991.724450483880.5545819909686.24438165312-0.6647215067090.5266254399791.71298790246-0.3909344876120.7765926229180.0579490899628-0.776382003089-0.0887471677851-0.09578587876420.42057645296-0.0578780017892-0.04317836789550.5762016020850.09142840802441.16880761417-9.933066208576.44070135364-61.2893495176
130.897200805138-1.66267630947-1.556269989995.16371138777-0.7379619727888.09392139274-0.8915402862110.00869978811918-1.35958794571-0.3726008604780.72637171048-0.309593825004-0.318112597945-0.03423780976220.2604220091930.426283973925-0.137286892433-0.0003064014223430.474745467693-0.03056229381931.10789601098-9.840125996434.89124560876-61.982554663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'X' and (resid 1 through 34 )
2X-RAY DIFFRACTION2chain 'X' and (resid 35 through 146 )
3X-RAY DIFFRACTION3chain 'X' and (resid 147 through 179 )
4X-RAY DIFFRACTION4chain 'X' and (resid 180 through 227 )
5X-RAY DIFFRACTION5chain 'X' and (resid 228 through 258 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1 through 14 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 14 )
8X-RAY DIFFRACTION8chain 'Y' and (resid 1 through 55 )
9X-RAY DIFFRACTION9chain 'Y' and (resid 56 through 179 )
10X-RAY DIFFRACTION10chain 'Y' and (resid 180 through 227 )
11X-RAY DIFFRACTION11chain 'Y' and (resid 228 through 258 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 14 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1 through 14 )

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