[English] 日本語
Yorodumi
- PDB-4r6d: Modified mTFP* for enhanced metal binding: co-crystallization wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r6d
TitleModified mTFP* for enhanced metal binding: co-crystallization with CuCl2
ComponentsGFP-like fluorescent chromoprotein cFP484
KeywordsFLUORESCENT PROTEIN / beta barrel topology / engineered metalloenzyme / Diels-Alderase
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / GFP-like fluorescent chromoprotein cFP484
Similarity search - Component
Biological speciesClavularia sp. (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFischer, J. / Quitterer, F. / Groll, M. / Eppinger, J.
CitationJournal: TO BE PUBLISHED
Title: Modified mTFP* for enhanced metal binding: co-crystallization with CuCl2
Authors: Fischer, J. / Quitterer, F. / Groll, M. / Eppinger, J.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GFP-like fluorescent chromoprotein cFP484
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9523
Polymers24,8251
Non-polymers1272
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.198, 67.656, 84.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GFP-like fluorescent chromoprotein cFP484


Mass: 24825.068 Da / Num. of mol.: 1 / Fragment: unp residues 44-258
Mutation: H63Y, H80N, L82I, S100T, N101T, Q104A, L110F, A118P, D119N, M151L, R161Y, F162L, D163K, M165E, L179T, K180G, E182D, P183A, I187R, V196K, I199V, S200K, S202K, H210Y, C213V, S217T, K220R, ...Mutation: H63Y, H80N, L82I, S100T, N101T, Q104A, L110F, A118P, D119N, M151L, R161Y, F162L, D163K, M165E, L179T, K180G, E182D, P183A, I187R, V196K, I199V, S200K, S202K, H210Y, C213V, S217T, K220R, V224A, I239C, Y246H, L251V, N254S, Y259N, L261T, L262F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clavularia sp. (invertebrata) / Plasmid: pET303 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q9U6Y3
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25.9% PEG3000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 6, 2014
RadiationMonochromator: BRUKER MICROSTAR MICRO-FOCUS (MONTEL OPTICS) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→70 Å / Num. all: 32546 / Num. obs: 32526 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.7.0032refinement
PROTEUM PLUSPLUSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4Q9W

4q9w


Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.44 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19397 1642 5.1 %RANDOM
Rwork0.15066 ---
obs0.1529 30761 99.75 %-
all-32403 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2--0.46 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 2 310 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191816
X-RAY DIFFRACTIONr_bond_other_d0.0010.021699
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9752457
X-RAY DIFFRACTIONr_angle_other_deg0.75633937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08524.41986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18515319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.615158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_mcbond_it1.2551.011864
X-RAY DIFFRACTIONr_mcbond_other1.2551.01863
X-RAY DIFFRACTIONr_mcangle_it1.4941.521081
X-RAY DIFFRACTIONr_mcangle_other1.4941.5211082
X-RAY DIFFRACTIONr_scbond_it1.8811.315952
X-RAY DIFFRACTIONr_scbond_other1.8811.315952
X-RAY DIFFRACTIONr_scangle_other2.0761.8421374
X-RAY DIFFRACTIONr_long_range_B_refined3.50710.7552270
X-RAY DIFFRACTIONr_long_range_B_other2.6469.4942106
X-RAY DIFFRACTIONr_rigid_bond_restr2.34533514
X-RAY DIFFRACTIONr_sphericity_free32.773571
X-RAY DIFFRACTIONr_sphericity_bonded9.34253707
LS refinement shellResolution: 1.55→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 107 -
Rwork0.294 2209 -
obs--99.31 %
Refinement TLS params.Method: refined / Origin x: 15.9045 Å / Origin y: -2.5472 Å / Origin z: -3.564 Å
111213212223313233
T0.0014 Å20.0008 Å2-0.0005 Å2-0.0128 Å2-0 Å2--0.0084 Å2
L0.035 °2-0.0088 °2-0.0084 °2-0.0128 °2-0.0074 °2--0.0657 °2
S0.0022 Å °-0.001 Å °0.001 Å °-0.0036 Å °-0.0013 Å °0.0019 Å °0.0069 Å °0.0007 Å °-0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 217
2X-RAY DIFFRACTION1A901 - 902
3X-RAY DIFFRACTION1A1001 - 1310

+
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