[English] 日本語
Yorodumi
- PDB-3wvq: Structure of ATP grasp protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wvq
TitleStructure of ATP grasp protein
ComponentsPGM1
KeywordsBIOSYNTHETIC PROTEIN / ATP grasp domain / LIGASE
Function / homologyPre ATP-grasp domain / PGM1 C-terminal domain / PGM1 C-terminal domain / Pre ATP-grasp domain / ATP-grasp fold / ATP-grasp fold profile. / ATP binding / metal ion binding / PGM1
Function and homology information
Biological speciesStreptomyces cirratus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.955 Å
AuthorsMatsui, T. / Noike, M. / Ooya, K. / Sasaki, I. / Hamano, Y. / Maruyama, C. / Ishikawa, J. / Satoh, Y. / Ito, H. / Dairi, T. / Morita, H.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin.
Authors: Noike, M. / Matsui, T. / Ooya, K. / Sasaki, I. / Ohtaki, S. / Hamano, Y. / Maruyama, C. / Ishikawa, J. / Satoh, Y. / Ito, H. / Morita, H. / Dairi, T.
History
DepositionJun 4, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PGM1
B: PGM1
C: PGM1
D: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,09021
Polymers194,4654
Non-polymers1,62517
Water23,4011299
1
A: PGM1
B: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,99710
Polymers97,2322
Non-polymers7658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PGM1
D: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,09311
Polymers97,2322
Non-polymers8619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9044
Polymers48,6161
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0926
Polymers48,6161
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2858
Polymers48,6161
Non-polymers6687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8083
Polymers48,6161
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.660, 86.750, 94.260
Angle α, β, γ (deg.)73.740, 85.930, 68.260
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
PGM1


Mass: 48616.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cirratus (bacteria) / Strain: MD227-A9 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0A6YVN3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1299 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1M Tris-HCl, pH 8.3, 1.175M Lithium Sulfate, 10mM L-Met, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 14, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 154262 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.011 / Net I/σ(I): 9.94
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-2.070.7940.6192.3118375251370470970.71791.7
2.07-2.220.8910.4173.4418637348298468150.48296.9
2.22-2.390.9380.2974.7217311844694434910.34397.3
2.39-2.620.9640.2176.3416071641394403960.25197.6
2.62-2.930.9830.1468.9614511137310365260.16997.9
2.93-3.380.9930.08814.4312818033016324160.10298.2
3.38-4.130.9960.05422.2110756027844274130.06398.5
4.13-5.820.9970.04426.658306621558212430.05198.5
5.82-500.9980.03829.964548712022117580.04597.8

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVEphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.955→45.177 Å / SU ML: 0.22 / σ(F): 1.92 / Phase error: 24.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 7713 5 %random
Rwork0.1943 ---
obs0.1961 154238 97.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 269.01 Å2 / Biso mean: 22.2453 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: LAST / Resolution: 1.955→45.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13068 0 87 1299 14454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813433
X-RAY DIFFRACTIONf_angle_d1.0618273
X-RAY DIFFRACTIONf_chiral_restr0.0421997
X-RAY DIFFRACTIONf_plane_restr0.0052406
X-RAY DIFFRACTIONf_dihedral_angle_d13.5964804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.955-1.97720.32822010.27493811401275
1.9772-2.00050.29412550.25144834508997
2.0005-2.02490.31972560.23574865512197
2.0249-2.05050.28322560.22914876513297
2.0505-2.07750.25982550.23024841509697
2.0775-2.10590.28642590.22824916517597
2.1059-2.1360.25152560.22034858511497
2.136-2.16790.27812560.21674879513597
2.1679-2.20180.27482570.2124868512597
2.2018-2.23790.27452590.2074921518097
2.2379-2.27650.21772580.19284901515997
2.2765-2.31780.24152560.1964872512898
2.3178-2.36240.24642600.19834943520398
2.3624-2.41060.24622590.20064921518098
2.4106-2.46310.2472580.20094890514898
2.4631-2.52030.24982580.20234916517498
2.5203-2.58340.24042600.20734927518798
2.5834-2.65320.25692580.20634911516998
2.6532-2.73130.26442610.21124962522398
2.7313-2.81940.22472580.21574885514398
2.8194-2.92020.26542610.20954966522798
2.9202-3.03710.27142610.21014951521299
3.0371-3.17530.24412600.20684956521699
3.1753-3.34260.24482620.19554962522499
3.3426-3.5520.21462610.18024962522399
3.552-3.82610.19822610.16354972523399
3.8261-4.21090.16712630.16074987525099
4.2109-4.81960.17692630.15624989525299
4.8196-6.06980.20782620.17684987524999
6.0698-45.1890.19082630.18064996525999

+
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://pdbjlvh1.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