[English] 日本語
Yorodumi
- PDB-6dp7: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dp7
TitleCrystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 500 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Components
  • DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')
  • RNA (5'-R(*AP*CP*AP*U)-3')
  • RNA (5'-R(P*CP*G)-3')
  • Ribonuclease H
KeywordsHYDROLASE/DNA/RNA / protein-RNA-DNA complex / double helix / RNA hydrolysis / in crystallo catalysis / metal dependent catalysis / monovalent cations / divalent cations / HYDROLASE-DNA-RNA complex
Function / homology
Function and homology information


DNA replication, removal of RNA primer / 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 / Ribonuclease H1 N-terminal domain / : / 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, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / 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 / MOLECULAR REPLACEMENT / Resolution: 1.381 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 1.1Oct 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_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.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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,00614
Polymers19,2424
Non-polymers76410
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-37 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.013, 37.557, 61.932
Angle α, β, γ (deg.)90.000, 96.790, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
RNA chain , 2 types, 2 molecules Bb

#2: RNA chain RNA (5'-R(*AP*CP*AP*U)-3')


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


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

-
Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Ribonuclease H / RNase H


Mass: 15587.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: rnhA, BH0863 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / 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)

-
Non-polymers , 5 types, 179 molecules

#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsNote that chain B was split into 2 chains (B and b) at the position 4-5, where the cleavage does occur

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.9 % / Mosaicity: 0 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 20% glycerol, 200 mM KI, and 25 mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→17.98 Å / Num. obs: 38088 / % possible obs: 98.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 17.21 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.061 / Rrim(I) all: 0.086 / Net I/σ(I): 10.1 / Num. measured all: 74048
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.296 / Num. measured all: 2990 / Num. unique obs: 1523 / CC1/2: 0.763 / Rpim(I) all: 0.296 / Rrim(I) all: 0.419 / Net I/σ(I) obs: 4.1 / % possible all: 76.4

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZBL

1zbl


Resolution: 1.381→17.983 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 1908 5.04 %
Rwork0.1686 35979 -
obs0.1698 37887 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.9 Å2 / Biso mean: 29.3649 Å2 / Biso min: 12.39 Å2
Refinement stepCycle: final / Resolution: 1.381→17.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 244 16 169 1529
Biso mean--58.98 39.56 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071426
X-RAY DIFFRACTIONf_angle_d0.9461969
X-RAY DIFFRACTIONf_chiral_restr0.073217
X-RAY DIFFRACTIONf_plane_restr0.006207
X-RAY DIFFRACTIONf_dihedral_angle_d23.788549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3807-1.41520.30051280.24652161228983
1.4152-1.45350.27351410.24812599274099
1.4535-1.49620.29411210.23852571269299
1.4962-1.54450.22521480.23672559270798
1.5445-1.59960.20291240.194226012725100
1.5996-1.66360.21351180.179426302748100
1.6636-1.73930.20211450.177826262771100
1.7393-1.83090.22161410.177226012742100
1.8309-1.94550.26261250.22312570269598
1.9455-2.09550.1971420.176226122754100
2.0955-2.3060.18551350.176426332768100
2.306-2.63880.16431540.158526252779100
2.6388-3.32120.16361420.157126522794100
3.3212-17.98410.18171440.13972539268394
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)
13.8197-0.03771.57548.765-2.86292.74360.08810.33560.1769-0.82940.0056-1.46330.00321.98490.26720.23790.05140.06850.5174-0.05050.310640.675-4.27318.623
24.8076-2.25464.81382.1723-2.06844.93540.32830.1314-0.4796-0.2138-0.04090.12120.3599-0.1526-0.33520.2010.00180.01090.1888-0.01080.141119.716-6.12116.521
32.0024-0.7884-0.21772.01872.03342.5550.1012-0.2136-1.7450.1007-0.1155-0.41780.58990.40320.1150.24380.06880.02810.27060.030.328327.981-11.66523.753
45.4480.01963.40912.22440.36634.96270.0426-0.3392-0.1429-0.0264-0.09780.08970.0926-0.58480.03260.10570.00630.03880.1449-0.00270.08318.095-0.95822.306
54.3695-1.05732.19323.10970.90174.36590.0907-0.33-0.04280.1235-0.0145-0.22310.4138-0.083-0.04520.1154-0.00170.0330.16980.020.107731.146-1.10225.288
68.9191-6.395-2.25997.60573.67152.32340.16130.2310.7337-0.3288-0.0519-0.6413-0.70360.3228-0.15650.2562-0.00520.0540.13670.02950.147723.9599.47116.624
75.6295-0.90594.06587.84240.97048.34310.05420.07370.4592-0.3623-0.30710.7589-0.2835-0.63410.18650.22390.1621-0.00020.3078-0.09810.20358.5967.76216.126
82.78973.19391.94574.33953.53037.4550.0372-0.45680.30560.0068-0.33890.1762-0.252-0.83710.32780.18620.0648-0.00210.2415-0.0460.148813.2196.51625.533
93.74570.20180.55315.56134.95954.51130.0761-0.86591.04070.23770.3537-0.638-0.12630.8671-0.340.2259-0.0213-0.00930.25660.00650.240228.4747.32429.944
100.4038-0.9826-1.19114.13965.93348.78240.23130.59690.055-0.5343-0.122-0.4807-0.31130.3665-0.16660.22350.04780.08450.33890.02250.171834.447-0.93312.14
115.22471.0068-4.39527.15881.70514.63470.19450.6405-0.7039-0.2731-0.21940.08330.30120.05630.00720.25410.0715-0.01210.2444-0.05580.164525.529-9.75712.266
121.5058-1.8712.65255.9214-3.16155.48740.28080.09520.0397-0.5396-0.6696-0.4994-0.01140.49630.33740.30170.08350.08030.24310.03090.155723.9061.2694.468
131.2053-1.7941-2.86614.063.22727.62420.08150.16340.063-1.1326-0.55840.3238-0.8268-0.5920.39130.41660.094-0.03530.22690.00520.123416.4513.7983.062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 61:66 )A61 - 66
2X-RAY DIFFRACTION2( CHAIN A AND RESID 67:87 )A67 - 87
3X-RAY DIFFRACTION3( CHAIN A AND RESID 88:96 )A88 - 96
4X-RAY DIFFRACTION4( CHAIN A AND RESID 97:122 )A97 - 122
5X-RAY DIFFRACTION5( CHAIN A AND RESID 123:133 )A123 - 133
6X-RAY DIFFRACTION6( CHAIN A AND RESID 134:142 )A134 - 142
7X-RAY DIFFRACTION7( CHAIN A AND RESID 143:155 )A143 - 155
8X-RAY DIFFRACTION8( CHAIN A AND RESID 156:171 )A156 - 171
9X-RAY DIFFRACTION9( CHAIN A AND RESID 172:177 )A172 - 177
10X-RAY DIFFRACTION10( CHAIN A AND RESID 178:186 )A178 - 186
11X-RAY DIFFRACTION11( CHAIN A AND RESID 187:195 )A187 - 195
12X-RAY DIFFRACTION12( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )B1 - 4
13X-RAY DIFFRACTION12( CHAIN B AND RESID 1:4 ) OR ( CHAIN b AND RESID 5:6 )b5 - 6
14X-RAY DIFFRACTION13( CHAIN C AND RESID 1:6 )C1 - 6

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more