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- PDB-6dp5: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Compl... -

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Basic information

Entry
Database: PDB / ID: 6dp5
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 40 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Components
  • 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
  • 5'-R(P*CP*G)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
  • DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
  • Ribonuclease H
KeywordsHYDROLASE/DNA/RNA / protein-RNA-DNA complex / RNA hydrolysis / in crystallo catalysis / metal dependent catalysis / HYDROLASE-DNA-RNA complex
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily ...Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / : / DNA / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.432 Å
AuthorsSamara, N.L. / Yang, W.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Cation trafficking propels RNA hydrolysis.
Authors: Samara, N.L. / Yang, W.
History
DepositionJun 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 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 / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _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_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
B: 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
b: 5'-R(P*CP*G)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'
C: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,09119
Polymers19,9854
Non-polymers1,10615
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-38 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.899, 37.505, 62.254
Angle α, β, γ (deg.)90.000, 96.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

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Components

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RNA chain , 2 types, 2 molecules Bb

#2: RNA chain 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'


Mass: 1224.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain 5'-R(P*CP*G)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3'


Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Ribonuclease H / RNase H


Mass: 16330.462 Da / Num. of mol.: 1 / Fragment: Catalytic Domain residues 59-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: rnhA, BH0863 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KEI9, ribonuclease H
#4: DNA chain DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')


Mass: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 162 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.45 Å3/Da / Density % sol: 49.72 % / Mosaicity: 0 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 20% glycerol, 200 mM KI, and 25 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→20.01 Å / Num. obs: 32560 / % possible obs: 93.8 % / Redundancy: 1 % / Biso Wilson estimate: 19.2 Å2 / Net I/σ(I): 6.8 / Num. measured all: 32560
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
1.43-1.4611325176.4
7.84-20.011218192.3

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementStarting model: 1ZBL
Resolution: 1.432→20.008 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.35
Details: Structures refined in Phenix and nucleic acid and protein residues built in Coot
RfactorNum. reflection% reflection
Rfree0.1759 3264 5.13 %
Rwork0.1527 --
obs0.1539 32560 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.23 Å2 / Biso mean: 29.2611 Å2 / Biso min: 13.22 Å2
Refinement stepCycle: final / Resolution: 1.432→20.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 244 37 147 1538
Biso mean--60.54 37.83 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091490
X-RAY DIFFRACTIONf_angle_d1.1982045
X-RAY DIFFRACTIONf_chiral_restr0.083226
X-RAY DIFFRACTIONf_plane_restr0.007213
X-RAY DIFFRACTIONf_dihedral_angle_d22.415587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4319-1.45330.37141190.31852180229976
1.4533-1.4760.33341290.29542273240284
1.476-1.50020.23661170.27072684280193
1.5002-1.52610.25141310.25272653278496
1.5261-1.55380.28491510.22912761291296
1.5538-1.58370.22731780.20182668284698
1.5837-1.6160.22121550.18922726288198
1.616-1.65110.22271180.17762724284297
1.6511-1.68950.24521390.16922690282996
1.6895-1.73170.18791650.1652734289997
1.7317-1.77850.17921530.15532629278296
1.7785-1.83080.20241420.16052683282595
1.8308-1.88990.21261380.17212589272793
1.8899-1.95740.21981250.18852501262688
1.9574-2.03570.17441180.1522484260289
2.0357-2.12820.18041420.1572658280095
2.1282-2.24030.18911350.14822713284896
2.2403-2.38040.191510.15462685283696
2.3804-2.56390.18351470.14862661280896
2.5639-2.82120.17621720.15162690286296
2.8212-3.2280.16581130.14812689280295
3.228-4.06140.14631220.12572568269091
4.0614-20.00950.13432040.12292680288498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.24410.4548-1.79698.7712-1.59882.7144-0.21250.18680.1566-0.4074-0.3743-0.96730.10011.57380.48520.18920.04760.0390.49060.03690.297540.8618-4.411819.0103
27.7987-1.50855.39522.8156-0.57255.16480.32420.1308-0.2202-0.2474-0.1750.15760.3478-0.0728-0.14290.21060.01480.00650.19820.00380.154821.5537-6.336516.3162
34.0394-0.4011.73321.2518-0.44463.66540.0827-0.087-0.1562-0.0671-0.0541-0.01040.03-0.05-0.02950.14650.01620.02770.11970.00050.117222.4246-1.783121.6044
44.8083-1.96143.41031.5738-2.12357.0919-0.10190.1170.5423-0.2284-0.02870.4561-0.3232-0.48550.08920.23080.12790.01990.2301-0.07280.19638.85427.91415.94
55.65514.84397.28085.86555.67119.59410.1137-0.40050.18840.0483-0.2720.1534-0.191-0.52080.15250.18550.04610.01880.1974-0.02320.163412.58335.848624.8787
63.938-1.1841-1.74153.68142.40385.94580.11630.3006-0.1026-0.3573-0.0109-0.1795-0.02770.3213-0.14350.13520.0537-0.01510.14520.04710.094628.9293-1.024317.7961
72.6420.16162.26968.4221-2.01862.70780.0870.4409-0.0647-0.6746-0.3018-0.25930.13010.21430.2170.27950.07350.05940.26650.01770.14923.84620.68665.0039
83.546-0.9714-2.43464.72483.95058.8641-0.02350.2376-0.104-0.959-0.33790.1969-0.408-0.31940.36480.36450.0623-0.02630.22020.0170.129316.51733.56843.2054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 66 )A61 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 75 )A67 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 142 )A76 - 142
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 155 )A143 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 169 )A156 - 169
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 196 )A170 - 196
7X-RAY DIFFRACTION7(chain 'B' and (resid 1 through 4 )) OR (chain 'b' and (resid 5 through 6 ))B1 - 4
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 6 )C1 - 6

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