[English] 日本語
Yorodumi
- PDB-4z20: Crystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z20
TitleCrystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable DNA with a TTGT Central Four
Components
  • (DNA (26-MER)) x 2
  • MEGANUCLEASE I-SMAMI
Keywordshydrolase/dna / Hydrolase-DNA complex / LAGLIDADG / homing endonuclease / meganuclease
Function / homology
Function and homology information


endonuclease activity / mitochondrion / metal ion binding
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Homing endonuclease LAGLIDADG domain-containing protein
Similarity search - Component
Biological speciesSordaria macrospora (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHallinan, J.P. / Stoddard, B.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2016
Title: Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.
Authors: Lambert, A.R. / Hallinan, J.P. / Shen, B.W. / Chik, J.K. / Bolduc, J.M. / Kulshina, N. / Robins, L.I. / Kaiser, B.K. / Jarjour, J. / Havens, K. / Scharenberg, A.M. / Stoddard, B.L.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MEGANUCLEASE I-SMAMI
C: DNA (26-MER)
B: DNA (26-MER)
D: MEGANUCLEASE I-SMAMI
F: DNA (26-MER)
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,87711
Polymers100,5206
Non-polymers3565
Water19811
1
A: MEGANUCLEASE I-SMAMI
C: DNA (26-MER)
B: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3925
Polymers50,2603
Non-polymers1322
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MEGANUCLEASE I-SMAMI
F: DNA (26-MER)
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4846
Polymers50,2603
Non-polymers2243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.690, 172.262, 59.994
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12C
22F
13B
23E

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLYAA8 - 3009 - 301
21LEULEUGLYGLYDD8 - 3009 - 301
12DCDCDCDCCB1 - 261 - 26
22DCDCDCDCFE1 - 261 - 26
13DGDGDGDGBC1 - 261 - 26
23DGDGDGDGEF1 - 261 - 26

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.173049, -0.000417, -0.984913), (-0.016108, -0.999865, 0.003253), (-0.984781, 0.016428, 0.173019)77.233177, 33.690708, 76.140663
3given(1), (1), (1)
4given(-0.183606, 7.8E-5, -0.983), (-0.009019, -0.999958, 0.001605), (-0.982958, 0.009161, 0.183599)77.169601, 33.869049, 75.989754
5given(1), (1), (1)
6given(-0.187852, -0.000228, -0.982197), (-0.012371, -0.99992, 0.002598), (-0.982119, 0.012639, 0.187834)77.078827, 33.792938, 75.68586

-
Components

-
Protein , 1 types, 2 molecules AD

#1: Protein MEGANUCLEASE I-SMAMI


Mass: 34283.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell) (fungus)
Strain: ATCC MYA-333 / DSM 997 / K(L3346) / K-hell / Gene: SMAC_12671 / Production host: Escherichia coli (E. coli) / References: UniProt: F7WD42

-
DNA chain , 2 types, 4 molecules CFBE

#2: DNA chain DNA (26-MER)


Mass: 7850.054 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8126.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 16 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 25% PEG 2000 MME, 5mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→86.13 Å / Num. obs: 18370 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.039 / Rrim(I) all: 0.075 / Χ2: 1.297 / Net I/av σ(I): 16.928 / Net I/σ(I): 19.3 / Num. measured all: 69222
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.113.70.79518010.8050.4780.9291.51198.3
3.11-3.233.80.48718480.9430.290.5671.48798.6
3.23-3.383.80.22918070.9920.1390.2681.54598.7
3.38-3.563.80.1918380.9910.1150.2221.46399.1
3.56-3.783.80.16218290.9940.0960.1881.43499
3.78-4.073.80.10118400.9950.060.1181.21499.1
4.07-4.483.80.06618300.9970.0390.0771.09499
4.48-5.133.80.04318670.9980.0260.0511.03999.7
5.13-6.463.80.03818410.9980.0230.0451.18299.2
6.46-503.70.02518690.9990.0150.0291.00998.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOX

4lox


Resolution: 3.2→86.13 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 87.311 / SU ML: 0.645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.638 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2912 753 5 %RANDOM
Rwork0.2333 ---
obs0.2361 14420 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 439.61 Å2 / Biso mean: 188.585 Å2 / Biso min: 99.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å2-2.08 Å2
2--1.2 Å20 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 3.2→86.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 2132 20 11 6503
Biso mean--428.3 429.34 -
Num. residues----693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0166849
X-RAY DIFFRACTIONr_bond_other_d0.0060.025220
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.6629737
X-RAY DIFFRACTIONr_angle_other_deg1.918312026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4623.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1915644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5981513
X-RAY DIFFRACTIONr_chiral_restr0.0820.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026364
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021581
X-RAY DIFFRACTIONr_mcbond_it4.4499.7042351
X-RAY DIFFRACTIONr_mcbond_other4.4459.7032350
X-RAY DIFFRACTIONr_mcangle_it7.32914.5572932
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A22507.45
2C4806.36
3B46813.87
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 56 -
Rwork0.321 1046 -
all-1102 -
obs--99.01 %
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)
10.77910.12670.29074.16940.30010.1445-0.04340.43570.03030.0530.15440.3862-0.03830.159-0.1111.3440.01730.08670.9392-0.05111.05513.1162.720689.3181
20.61820.02150.36270.0618-0.04030.43280.29160.24640.14480.2792-0.10520.02020.12120.4749-0.18641.548-0.01290.08050.6758-0.05971.219823.51855.247890.4198
30.80430.62380.73190.93780.50090.82160.4230.4060.03261.14720.0153-0.14250.14840.4008-0.43831.9948-0.01790.20820.30660.03421.261623.49952.186891.3818
40.37630.47630.36893.1509-0.33220.6799-0.0975-0.019-0.0488-0.00350.06320.0722-0.03330.16190.03431.3213-0.01830.1580.82550.12281.1688-0.979431.427464.872
50.021-0.12720.0222.4961-0.32571.15850.0308-0.03660.1033-0.2792-0.1880.09610.1695-0.12530.15711.37960.001-0.00120.50730.06891.4256-4.069128.74755.3449
60.1166-0.02660.3770.044-0.11141.4737-0.02740.0435-0.0253-0.1742-0.0370.15630.09570.43540.06441.63790.06450.07220.36420.19281.5771-4.952631.808955.4926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 302
2X-RAY DIFFRACTION2C1 - 26
3X-RAY DIFFRACTION3B1 - 26
4X-RAY DIFFRACTION4D8 - 301
5X-RAY DIFFRACTION5F1 - 26
6X-RAY DIFFRACTION6E1 - 26

+
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