[English] 日本語
Yorodumi
- PDB-3kdg: C-terminal domain of Bacillus subtilis MutL crystal form II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kdg
TitleC-terminal domain of Bacillus subtilis MutL crystal form II
ComponentsDNA mismatch repair protein mutL
KeywordsHYDROLASE / Mismatch repair / MutL / endonuclease / DNA damage / DNA repair
Function / homology
Function and homology information


mismatch repair complex / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / ATP binding
Similarity search - Function
MutL, C-terminal domain, regulatory subdomain / MutL, C-terminal domain, dimerisation subdomain / DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / formyl-coa transferase, domain 3 / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain ...MutL, C-terminal domain, regulatory subdomain / MutL, C-terminal domain, dimerisation subdomain / DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / formyl-coa transferase, domain 3 / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / Ribosomal Protein S8; Chain: A, domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuarne, A. / Pillon, M.C.
CitationJournal: Mol.Cell / Year: 2010
Title: Structure of the endonuclease domain of MutL: unlicensed to cut.
Authors: Pillon, M.C. / Lorenowicz, J.J. / Uckelmann, M. / Klocko, A.D. / Mitchell, R.R. / Chung, Y.S. / Modrich, P. / Walker, G.C. / Simmons, L.A. / Friedhoff, P. / Guarne, A.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA mismatch repair protein mutL
B: DNA mismatch repair protein mutL


Theoretical massNumber of molelcules
Total (without water)45,7342
Polymers45,7342
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-24 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.417, 74.335, 182.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA mismatch repair protein mutL /


Mass: 22867.223 Da / Num. of mol.: 2 / Fragment: residues 434-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU17050, mutL / Plasmid: pProEX HTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P49850
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 25% PEG 3350, 0.2 NaCl, 0.1 M TRIS pH 7.0 , VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 60242 / Num. obs: 60242 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 27.74 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.059 / Net I/σ(I): 25.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2951 / Rsym value: 0.69 / % possible all: 100

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GAB

3gab


Resolution: 2→38.88 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 3049 5.08 %random
Rwork0.1906 ---
obs0.1925 60020 99.15 %-
all-60242 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.559 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 41.225 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0 Å2
2--2.001 Å2-0 Å2
3----0.831 Å2
Refinement stepCycle: LAST / Resolution: 2→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 0 190 3279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053173
X-RAY DIFFRACTIONf_angle_d0.8754280
X-RAY DIFFRACTIONf_dihedral_angle_d17.3881210
X-RAY DIFFRACTIONf_chiral_restr0.057460
X-RAY DIFFRACTIONf_plane_restr0.004558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.01740.30381190.22842214221487
2.0174-2.05050.24391420.21352617261799
2.0505-2.08580.20661550.194126582658100
2.0858-2.12380.22921250.198625582558100
2.1238-2.16460.24821420.19522549254999
2.1646-2.20880.25361380.192226662666100
2.2088-2.25680.2455890.189426272627100
2.2568-2.30930.21551430.18425972597100
2.3093-2.3670.23481230.18626222622100
2.367-2.4310.23931490.19662582258299
2.431-2.50260.25511370.210126322632100
2.5026-2.58330.22761480.191826032603100
2.5833-2.67560.26351750.204425272527100
2.6756-2.78270.2571490.207726692669100
2.7827-2.90930.23371370.212125732573100
2.9093-3.06270.26521310.215126262626100
3.0627-3.25450.22381140.200426372637100
3.2545-3.50560.19571420.181325902590100
3.5056-3.85810.23331230.168326402640100
3.8581-4.41570.17761660.152325762576100
4.4157-5.56070.20411620.159726222622100
5.5607-38.88760.22631400.186725862586100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.4907-0.2073-0.2307-0.12261.01411.3543-0.0014-0.17870.2064-0.148-0.0889-0.0236-0.16840.01930.10250.05780.01380.01080.06080.02420.121419.49228.159511.2336
20.4268-0.5724-0.35240.28360.48210.0792-0.0426-0.0903-0.025-0.01070.0383-0.0186-0.04580.0019-0.00480.05110.0309-0.00610.06520.03150.063
30.70050.62540.76552.13350.56481.06510.4211-1.28970.60470.4362-0.46580.65910.933-0.38990.15390.36420.15120.10840.69310.03550.261
42.2369-0.3990.31990.27540.07830.43421.0486-1.22570.1799-0.02320.077-0.0555-1.21420.3111-0.76730.9237-0.2460.110.6995-0.19950.2591
5-0.6807-0.0492-0.3022-3.34731.7210.6113-0.0422-0.6020.31440.2907-0.0995-0.2394-0.8478-0.22720.08150.71990.09420.06520.6204-0.07660.2719
60.2479-0.1596-0.3543-0.09581.03460.31860.2958-0.7764-0.19270.5426-0.6307-0.3871-0.73781.18130.32290.5117-0.1341-0.08710.84330.10830.1902
71.85351.8374-2.65191.7480.42763.92920.4707-0.9042-0.1467-0.2606-0.8441-0.1056-0.88070.75450.28070.2921-0.0078-0.03070.31470.10390.1612
81.26240.2011-1.13221.37830.35360.8327-1.13410.6458-1.6675-0.19060.0458-0.29440.6798-0.64690.18-0.21610.3015-0.253-0.07870.4637-0.0527
90.5825-1.01070.02180.72580.23280.0406-0.0989-0.0305-0.0940.07750.18990.0574-0.0191-0.0873-0.07020.04230.02-0.01310.06510.02750.0992
100.0359-0.25980.29350.10490.29160.1786-0.01080.014-0.027-0.12750.0316-0.0821-0.0998-0.0294-0.02160.1326-0.0350.04150.06510.03930.1075
110.05580.581-1.1704-0.44551.1603-0.0941-0.2480.0736-0.1833-0.1023-0.0177-0.23290.19280.12280.16780.107-0.00230.02680.07630.02290.1323
120.5613-0.16460.06980.99390.2424-0.1245-0.0885-0.0252-0.2095-0.22460.10870.00860.0732-0.00670.04450.0730.01140.03620.01750.01030.1034
130.2928-0.6026-0.1730.66740.06820.2491-0.03960.06670.1098-0.0075-0.0344-0.0387-0.0756-0.02850.02960.1669-0.06860.0450.1004-0.04850.0882
141.3372-0.2095-0.04561.11370.55161.1496-0.01590.589-0.069-0.162-0.0805-0.04510.27340.08160.05340.1033-0.0371-0.01780.36170.04290.1154
151.55290.4148-1.17811.38960.09161.9106-0.01610.61690.0472-0.2561-0.0374-0.11130.2386-0.15170.04290.1875-0.00340.00760.2710.02120.1296
160.9738-0.41260.05051.0209-0.21840.85980.0581-0.25720.13930.3748-0.1291-0.0826-0.1781-0.0232-0.00910.1666-0.02820.02050.1118-0.00730.1236
172.4740.0718-0.93560.65090.09721.63840.38260.1285-0.32360.0784-0.1619-0.14340.3715-0.3323-0.2130.3186-0.1136-0.13710.25160.12280.3411
180.8526-0.5061-0.47190.23620.09290.8512-0.59-0.1318-0.1226-0.64010.4293-0.18840.86640.07350.09850.2887-0.07650.00950.02050.01430.1855
19-0.1116-0.35590.05691.03260.08450.03430.0372-0.0133-0.0206-0.11910.0072-0.2282-0.1313-0.2357-0.1150.0808-0.03050.047-0.00250.01480.1468
200.8622-0.2558-0.09723.2993-0.28391.1123-0.3039-0.23710.26050.03420.406-0.6718-0.017-0.0733-0.05510.1064-0.0105-0.05930.1424-0.01250.1762
Refinement TLS groupSelection details: chain B and resid 618:625)

+
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