[English] 日本語
Yorodumi
- PDB-4jca: Crystal Structure of the apo form of the evolved variant of the c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jca
TitleCrystal Structure of the apo form of the evolved variant of the computationally designed serine hydrolase, OSH55.4_H1. Northeast Structural Genomics Consortium (NESG) Target OR273
Componentsserine hydrolase
KeywordsHYDROLASE / 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 / CITRIC ACID / RUBIDIUM ION
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.411 Å
AuthorsKuzin, A.P. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Tong, S. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. ...Kuzin, A.P. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Tong, S. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Design of activated serine-containing catalytic triads with atomic-level accuracy.
Authors: Rajagopalan, S. / Wang, C. / Yu, K. / Kuzin, A.P. / Richter, F. / Lew, S. / Miklos, A.E. / Matthews, M.L. / Seetharaman, J. / Su, M. / Hunt, J.F. / Cravatt, B.F. / Baker, D.
History
DepositionFeb 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0863
Polymers17,8081
Non-polymers2782
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: serine hydrolase
hetero molecules

A: serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1726
Polymers35,6162
Non-polymers5554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area2200 Å2
ΔGint-25 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.870, 66.490, 65.690
Angle α, β, γ (deg.)90.00, 102.50, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein serine hydrolase / OSH55.4_H1


Mass: 17808.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others)
#2: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Rb
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 4.2
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: RbCl 0.1M, Sodium Citrate 0.1M, PEG 1000 40%, microbatch under oil, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 2, 2012
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: 2.4→30 Å / Num. obs: 11749 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 40.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.8

-
Processing

Software
NameVersionClassificationNB
PHENIXdev_1316refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ETJ

4etj


Resolution: 2.411→29.396 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.36 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 276 4.54 %
Rwork0.1777 --
obs0.181 6074 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.62 Å2
Refinement stepCycle: LAST / Resolution: 2.411→29.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 14 30 1233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071219
X-RAY DIFFRACTIONf_angle_d1.1331649
X-RAY DIFFRACTIONf_dihedral_angle_d12.971445
X-RAY DIFFRACTIONf_chiral_restr0.073187
X-RAY DIFFRACTIONf_plane_restr0.005216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4107-3.03670.28851490.20052823X-RAY DIFFRACTION97
3.0367-29.39810.23381270.172975X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -9.9622 Å / Origin y: 1.3494 Å / Origin z: -18.8879 Å
111213212223313233
T0.3161 Å2-0.0157 Å2-0.0022 Å2-0.3275 Å20.0105 Å2--0.2524 Å2
L3.1555 °21.1086 °20.128 °2-4.243 °20.4998 °2--2.6159 °2
S-0.0104 Å °-0.1119 Å °0.0282 Å °0.216 Å °-0.0348 Å °0.1699 Å °-0.053 Å °-0.0928 Å °0.0252 Å °
Refinement TLS groupSelection details: all

+
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