[English] 日本語
Yorodumi
- PDB-3tc6: Crystal Structure of Engineered Protein. Northeast Structural Gen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tc6
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR63.
ComponentsIndole-3-glycerol phosphate synthase
KeywordsLYASE / Structural Genomics / Engineered Protein / Northeast Structural Genomics Consortium / NESG / OR63 / PSI-Biology
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process
Similarity search - Function
Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Baker, D. ...Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.
Authors: Bjelic, S. / Kipnis, Y. / Wang, L. / Pianowski, Z. / Vorobiev, S. / Su, M. / Seetharaman, J. / Xiao, R. / Kornhaber, G. / Hunt, J.F. / Tong, L. / Hilvert, D. / Baker, D.
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Sep 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_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_ref_seq_dif.details / _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: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2457
Polymers29,6531
Non-polymers5926
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.933, 60.933, 118.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-672-

HOH

Detailsmonomer,30.47 kD,97.1%

-
Components

#1: Protein Indole-3-glycerol phosphate synthase / IGPS


Mass: 29653.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: trpC, SSO0895 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06121, indole-3-glycerol-phosphate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 5
Details: 40% PEG 400, 0.1 M Sodium phosphate monobasic, 0.1 M Sodium acetate, pH 5.0, Microbatch crystallization under oil, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 129900 / Num. obs: 129900 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.06 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.19 / Num. unique all: 12870 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1jul

1jul


Resolution: 1.6→31.633 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.93 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3296 5.08 %RANDOM
Rwork0.179 ---
obs0.18 64927 99.96 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.764 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso max: 64.03 Å2 / Biso mean: 19.468 Å2 / Biso min: 2.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.781 Å2-0 Å2-0 Å2
2--1.781 Å2-0 Å2
3----3.562 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 34 209 2247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152087
X-RAY DIFFRACTIONf_angle_d1.4972815
X-RAY DIFFRACTIONf_chiral_restr0.11323
X-RAY DIFFRACTIONf_plane_restr0.006355
X-RAY DIFFRACTIONf_dihedral_angle_d14.933826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.6230.2721330.24725152648
1.623-1.6470.2861390.25426282767
1.647-1.6730.2911410.24325182659
1.673-1.70.2611500.23325692719
1.7-1.730.21570.21925632720
1.73-1.7610.2221490.20725342683
1.761-1.7950.2071560.20525862742
1.795-1.8320.2341220.2125322654
1.832-1.8710.1941510.18825712722
1.871-1.9150.2371270.19125812708
1.915-1.9630.1841200.17526232743
1.963-2.0160.1631130.17825442657
2.016-2.0750.2091500.17425712721
2.075-2.1420.2081700.17225262696
2.142-2.2190.2011340.16425722706
2.219-2.3070.1951310.17425882719
2.307-2.4120.1751090.17525872696
2.412-2.5390.2431420.17426002742
2.539-2.6990.2231160.18625582674
2.699-2.9070.2221500.18725872737
2.907-3.1990.1731410.17525622703
3.199-3.6610.1671260.15625742700
3.661-4.6110.1561360.14725732709
4.611-31.6390.2021330.18825692702

+
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