[English] 日本語
Yorodumi
- PDB-4gvv: Crystal Structure of de novo design serine hydrolase OSH55.27, No... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gvv
TitleCrystal Structure of de novo design serine hydrolase OSH55.27, Northeast Structural Genomics Consortium (NESG) Target OR246
ComponentsDe novo design serine hydrolase
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG)
Function / homologyLeucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.895 Å
AuthorsKuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Kohan, E. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Kohan, E. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR246
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Kohan, E. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Dec 6, 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: De novo design serine hydrolase
B: De novo design serine hydrolase
C: De novo design serine hydrolase
D: De novo design serine hydrolase


Theoretical massNumber of molelcules
Total (without water)71,1884
Polymers71,1884
Non-polymers00
Water1,26170
1
A: De novo design serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7971
Polymers17,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: De novo design serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7971
Polymers17,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: De novo design serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7971
Polymers17,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: De novo design serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7971
Polymers17,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.634, 30.030, 128.868
Angle α, β, γ (deg.)90.000, 91.330, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer,15.64 kD,95.9%

-
Components

#1: Protein
De novo design serine hydrolase


Mass: 17796.961 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→29.63 Å / Num. obs: 12812 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 19.37 Å2 / Rmerge(I) obs: 0.178 / Net I/σ(I): 8.8

-
Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ESS

4ess


Resolution: 2.895→29.63 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.768 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.285 625 4.88 %random
Rwork0.186 ---
obs0.191 12804 99.84 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.395 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 83.06 Å2 / Biso mean: 14.703 Å2 / Biso min: 0.64 Å2
Baniso -1Baniso -2Baniso -3
1-6.048 Å2-0 Å20.345 Å2
2---5.006 Å2-0 Å2
3----1.042 Å2
Refinement stepCycle: LAST / Resolution: 2.895→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 0 70 4866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094872
X-RAY DIFFRACTIONf_angle_d1.1696586
X-RAY DIFFRACTIONf_chiral_restr0.071766
X-RAY DIFFRACTIONf_plane_restr0.004865
X-RAY DIFFRACTIONf_dihedral_angle_d17.1281775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.895-3.1860.3461520.2332967311999
3.186-3.6470.2811570.18230173174100
3.647-4.5920.2631640.16230173181100
4.592-29.6330.2711520.18431783330100

+
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