[English] 日本語
Yorodumi
- PDB-3fca: Genetic Incorporation of a Metal-ion Chelating Amino Acid into pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fca
TitleGenetic Incorporation of a Metal-ion Chelating Amino Acid into proteins as biophysical probe
ComponentsCysteine synthase
KeywordsTRANSFERASE / Phasing / Heavy metal / unnatural amino acid / metal binding
Function / homologyRossmann fold - #1100 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.149 Å
AuthorsWang, F. / Lee, H. / Spraggon, G. / Schultz, P.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Genetic incorporation of a metal-ion chelating amino acid into proteins as a biophysical probe.
Authors: Lee, H.S. / Spraggon, G. / Schultz, P.G. / Wang, F.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 27, 2024Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6064
Polymers62,4752
Non-polymers1312
Water2,954164
1
A: Cysteine synthase
B: Cysteine synthase
hetero molecules

A: Cysteine synthase
B: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,2118
Polymers124,9494
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10440 Å2
ΔGint-158 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.858, 135.858, 74.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

-
Components

#1: Protein Cysteine synthase / E.C.2.5.1.47 / TM0665


Mass: 31237.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): DH10B / References: cysteine synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCLOSEST REFERENCE WITH ONE CONFLICT IS TO Q9WZD3_THEMA Q9WZD3 FROM THERMOTOGA MARITIMA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 50% PEG 400, 200 mM NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 121 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.149→96.23 Å / Num. all: 354615 / Num. obs: 38516 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.085 / Net I/σ(I): 67.7
Reflection shellResolution: 2.149→2.23 Å / Redundancy: 9 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 20.2 / Num. unique all: 3661 / Rsym value: 0.185 / % possible all: 96.4

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 0 Å / D res low: 0 Å / FOM : 0 / Reflection: 0
Phasing dmFOM : 0.66 / FOM acentric: 0.67 / FOM centric: 0.63 / Reflection: 37023 / Reflection acentric: 33011 / Reflection centric: 4012
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.1-42.9620.910.940.8318011293508
3.8-6.10.910.930.8352384402836
3.1-3.80.850.860.7664325687745
2.7-3.10.730.740.5963445743601
2.3-2.70.550.560.421098010095885
2.2-2.30.320.330.2862285791437

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RESOLVE2.11phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.149→96.23 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 4.429 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1929 5 %RANDOM
Rwork0.207 ---
obs0.209 38407 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.29 Å2 / Biso mean: 29.044 Å2 / Biso min: 11.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.149→96.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 2 164 4542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224438
X-RAY DIFFRACTIONr_angle_refined_deg1.2282.0035978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2625576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22824.074162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32315814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2031530
X-RAY DIFFRACTIONr_chiral_restr0.0820.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023236
X-RAY DIFFRACTIONr_nbd_refined0.2280.22211
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23080
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.215
X-RAY DIFFRACTIONr_mcbond_it0.7311.52957
X-RAY DIFFRACTIONr_mcangle_it1.14424592
X-RAY DIFFRACTIONr_scbond_it1.8631663
X-RAY DIFFRACTIONr_scangle_it3.0194.51386
LS refinement shellResolution: 2.149→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 134 -
Rwork0.2 2592 -
all-2726 -
obs--96.63 %

+
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