[English] 日本語
Yorodumi
- PDB-2awa: Crystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2awa
TitleCrystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) (np_344555.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 2.50 A resolution
ComponentsDNA polymerase III, beta chain
KeywordsTRANSFERASE / np_344555.1 / DNA polymerase III / beta chain (EC 2.7.7.7) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of DNA polymerase III, beta chain (EC 2.7.7.7) (np_344555.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase III, beta chain
B: DNA polymerase III, beta chain
C: DNA polymerase III, beta chain
D: DNA polymerase III, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,1475
Polymers175,0554
Non-polymers921
Water4,522251
1
A: DNA polymerase III, beta chain
B: DNA polymerase III, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6203
Polymers87,5272
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-14 kcal/mol
Surface area34400 Å2
MethodPISA
2
C: DNA polymerase III, beta chain
D: DNA polymerase III, beta chain


Theoretical massNumber of molelcules
Total (without water)87,5272
Polymers87,5272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-13 kcal/mol
Surface area34180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.060, 70.720, 135.440
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 1 - 376 / Label seq-ID: 13 - 388

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
DNA polymerase III, beta chain /


Mass: 43763.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: dnaN / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: O06672, DNA-directed DNA polymerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.76 Å3/Da / Density % sol: 55.16 %
Description: THE EXPERIMENTAL MAD MAP IS POOR WITHOUT NCS AVERAGING. A MONOMER POLY-ALANINE MODEL OF 1MMI IS USED AS TEMPLATE FOR THE LOCATION OF FOUR MONOMERS IN THE EXPERIMENTAL MAP. THE MAD MAP IS ...Description: THE EXPERIMENTAL MAD MAP IS POOR WITHOUT NCS AVERAGING. A MONOMER POLY-ALANINE MODEL OF 1MMI IS USED AS TEMPLATE FOR THE LOCATION OF FOUR MONOMERS IN THE EXPERIMENTAL MAP. THE MAD MAP IS SIGNIFICANTLY IMPROVED WITH NCS AVERAGING WHICH ALLOWS THE COMPLETION OF THE MODEL FROM THE INITIAL PHASED MOLECULAR REPLACEMENT SOLUTION. THE IMPROVED PHASES RESULTING FROM NCS AVERAGING WERE USED AS PHASE RESTRAINTS IN THE REFMAC REFINEMENT.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 10.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97934, 0.91837, 0.97923
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 2, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.918371
30.979231
ReflectionResolution: 2.5→48.9 Å / Num. obs: 59570 / % possible obs: 91.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID
2.5-2.674.40.6781.8518897100041
2.6-2.7986.80.6782.4334577177561
2.79-2.9900.6783.161651884951
2.9-3.0392.10.6784.151737488721
3.03-3.1994.30.6785.631789291361
3.19-3.3995.50.6787.331819792801
3.39-3.6597.20.6789.861834793281
3.65-4.0197.40.678121840792901
4.01-4.5996.70.67814.951886694311
4.59-5.7595.90.67815.561856691921
5.75-48.993.10.67816.041887492621

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
MOLREPphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT
Starting model: 1MMI

1mmi


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 21.693 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.292
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. MANY SURFACE SIDE CHAINS ARE TRIMMED DUE TO LACK OF DEFINITIVE ELECTRON DENSITIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3044 5.1 %RANDOM
Rwork0.192 ---
all0.195 ---
obs-56494 48.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-2.72 Å2
2---2.04 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11381 0 6 251 11638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211558
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210748
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.96415724
X-RAY DIFFRACTIONr_angle_other_deg0.735324915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46751505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87425.174431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.183151981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3231545
X-RAY DIFFRACTIONr_chiral_restr0.0730.21990
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022153
X-RAY DIFFRACTIONr_nbd_refined0.2020.21926
X-RAY DIFFRACTIONr_nbd_other0.1730.210364
X-RAY DIFFRACTIONr_nbtor_refined0.1740.25674
X-RAY DIFFRACTIONr_nbtor_other0.0830.27488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2321
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0710.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.22
X-RAY DIFFRACTIONr_mcbond_it1.54237763
X-RAY DIFFRACTIONr_mcbond_other0.29133026
X-RAY DIFFRACTIONr_mcangle_it2.551512296
X-RAY DIFFRACTIONr_scbond_it4.65784175
X-RAY DIFFRACTIONr_scangle_it7.047113428
Refine LS restraints NCS

Ens-ID: 1 / Number: 5342 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.485
2Bloose positional0.475
3Cloose positional0.495
4Dloose positional0.545
1Aloose thermal2.0510
2Bloose thermal1.9710
3Cloose thermal2.0910
4Dloose thermal1.910
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 203 -
Rwork0.3 3580 -
obs--83.86 %
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)
13.94750.17930.00043.36120.15191.35930.04290.1761-0.0697-0.1293-0.0952-0.0066-0.0915-0.06220.0524-0.33040.00880.1127-0.31920.0051-0.413718.76836.102-9.22
22.37310.35580.64463.25551.45012.33710.0470.0924-0.1548-0.02680.0597-0.383-0.02060.2614-0.1067-0.3186-0.00850.0862-0.30620.012-0.220945.3940.0133.642
34.7236-0.2155-1.19242.43650.00123.61640.1022-0.38640.01670.2940.0302-0.16360.19090.3972-0.1324-0.1842-0.0134-0.0587-0.16420.0243-0.172746.47747.28131.188
46.6505-0.1760.38452.72410.1671.7343-0.299-0.56660.36650.12730.13720.0432-0.10780.11730.1618-0.09650.00860.0266-0.12580.0372-0.346119.34251.56244.119
52.35680.09141.48482.5539-0.46953.3884-0.1238-0.3977-0.07980.45550.0350.0683-0.1565-0.23810.0888-0.23680.01670.1585-0.15970.1031-0.3075-7.57947.22431.165
63.3608-0.6287-1.3422.84190.81393.91430.07270.0688-0.35410.0265-0.2280.21690.2157-0.2490.1553-0.3359-0.03570.073-0.23130.0046-0.204-8.36838.4134.323
77.29850.6622-0.05722.9792-0.03751.71470.02970.86990.3679-0.22710.1084-0.00510.0177-0.05-0.1381-0.00330.0183-0.1168-0.0770.0168-0.225722.72918.05424.357
83.1172-0.43930.73022.11370.18253.638-0.13640.32690.0731-0.53590.00850.1394-0.14830.27910.1279-0.1304-0.02280.0421-0.1555-0.068-0.270150.12211.35334.572
94.43120.9744-0.94723.235-1.26664.62980.1326-0.3869-0.3734-0.0215-0.2681-0.24130.32180.33990.1355-0.27930.03140.0815-0.0587-0.0052-0.26852.64-1.14460.058
106.52770.2124-0.04452.162-0.41772.6198-0.0283-0.4425-0.233-0.13650.00240.01180.00670.18720.0259-0.2801-0.02760.033-0.15770.0666-0.336926.758-5.88475.195
112.9563-0.45451.37243.027-1.07253.1931-0.0898-0.2793-0.0933-0.00770.04320.4854-0.1506-0.19490.0466-0.2070.0233-0.0411-0.2684-0.026-0.1464-0.4930.83864.973
124.21880.3473-0.4753.066-0.79124.3510.05110.27540.0707-0.28960.09930.18270.1603-0.3598-0.1504-0.04060.0012-0.2392-0.2565-0.0136-0.0988-3.01412.13138.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 12513 - 137
2X-RAY DIFFRACTION2AA126 - 256138 - 268
3X-RAY DIFFRACTION3AA257 - 377269 - 389
4X-RAY DIFFRACTION4BB0 - 12512 - 137
5X-RAY DIFFRACTION5BB126 - 256138 - 268
6X-RAY DIFFRACTION6BB257 - 376269 - 388
7X-RAY DIFFRACTION7CC1 - 12513 - 137
8X-RAY DIFFRACTION8CC126 - 256138 - 268
9X-RAY DIFFRACTION9CC257 - 377269 - 389
10X-RAY DIFFRACTION10DD0 - 12512 - 137
11X-RAY DIFFRACTION11DD126 - 256138 - 268
12X-RAY DIFFRACTION12DD257 - 376269 - 388

+
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