[English] 日本語
Yorodumi
- PDB-2p4m: High pH structure of Rtms5 H146S variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p4m
TitleHigh pH structure of Rtms5 H146S variant
ComponentsGFP-like non-fluorescent chromoprotein
KeywordsLUMINESCENT PROTEIN / beta barrel / GFP-like protein / chromophore / chromoprotein
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / GFP-like non-fluorescent chromoprotein
Similarity search - Component
Biological speciesMontipora efflorescens (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBattad, J.M. / Wilmann, P.G. / Olsen, S. / Byres, E. / Smith, S.C. / Dove, S.G. / Turcic, K.N. / Devenish, R.J. / Rossjohn, J. / Prescott, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A structural basis for the pH-dependent increase in fluorescence efficiency of chromoproteins
Authors: Battad, J.M. / Wilmann, P.G. / Olsen, S. / Byres, E. / Smith, S.C. / Dove, S.G. / Turcic, K.N. / Devenish, R.J. / Rossjohn, J. / Prescott, M.
History
DepositionMar 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GFP-like non-fluorescent chromoprotein
B: GFP-like non-fluorescent chromoprotein
C: GFP-like non-fluorescent chromoprotein
D: GFP-like non-fluorescent chromoprotein
E: GFP-like non-fluorescent chromoprotein
F: GFP-like non-fluorescent chromoprotein
G: GFP-like non-fluorescent chromoprotein
H: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,76732
Polymers198,7228
Non-polymers3,04624
Water22,6631258
1
A: GFP-like non-fluorescent chromoprotein
B: GFP-like non-fluorescent chromoprotein
C: GFP-like non-fluorescent chromoprotein
D: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,26419
Polymers99,3614
Non-polymers1,90415
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-42 kcal/mol
Surface area32080 Å2
MethodPISA
2
E: GFP-like non-fluorescent chromoprotein
F: GFP-like non-fluorescent chromoprotein
G: GFP-like non-fluorescent chromoprotein
H: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,50313
Polymers99,3614
Non-polymers1,1429
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-40 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.750, 186.319, 185.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
GFP-like non-fluorescent chromoprotein / Rtms 5 / Non-fluorescent pocilloporin


Mass: 24840.211 Da / Num. of mol.: 8 / Mutation: H146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Montipora efflorescens (invertebrata) / Strain: Nova Blue / Gene: Rtms5 / Plasmid: pQE10 / Production host: Escherichia coli (E. coli) / References: UniProt: P83690
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1258 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS BELIEVE THAT LYS A 36 IS CORRECT. GLN 66, TYR 67 AND GLY 68 ARE MODIFIED TO MAKE ...THE AUTHORS BELIEVE THAT LYS A 36 IS CORRECT. GLN 66, TYR 67 AND GLY 68 ARE MODIFIED TO MAKE CHROMOPHORE (CRQ 66).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.7
Details: PEG 3350, Potassium Iodide, Tris Buffer, pH 10.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 243612 / % possible obs: 90.2 %

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOV

1mov


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.522 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 8796 4 %RANDOM
Rwork0.226 ---
obs0.227 219698 90.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---1.05 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13920 0 24 1258 15202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214352
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.97119409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7551728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44224.615624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.363152352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1441540
X-RAY DIFFRACTIONr_chiral_restr0.0670.21968
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211108
X-RAY DIFFRACTIONr_nbd_refined0.1730.26153
X-RAY DIFFRACTIONr_nbtor_refined0.3020.29273
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3440.21305
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.245
X-RAY DIFFRACTIONr_mcbond_it0.2261.58729
X-RAY DIFFRACTIONr_mcangle_it0.376214024
X-RAY DIFFRACTIONr_scbond_it0.60336439
X-RAY DIFFRACTIONr_scangle_it0.9844.55385
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 379 -
Rwork0.358 9891 -
obs-10270 57.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29460.13970.93391.9127-0.05941.78130.0225-0.014-0.28970.0312-0.0105-0.1470.19690.1344-0.012-0.11160.04110.0636-0.1412-0.0191-0.091129.974163.647442.2212
20.7152-0.01920.18121.29330.3891.7968-0.05370.0255-0.08130.02950.0124-0.16550.01630.13990.0412-0.16910.00910.0155-0.14490.0186-0.1392129.726174.456246.7195
32.1591-0.3363-0.61291.36220.21282.0324-0.02030.09390.2292-0.0725-0.0587-0.1024-0.34880.10060.079-0.0166-0.056-0.1039-0.1379-0.0197-0.0309129.5959211.125952.0528
40.6610.0956-0.04441.25260.26271.9382-0.0923-0.0350.1192-0.009-0.0028-0.1557-0.1020.19690.0951-0.1415-0.0229-0.0443-0.14350.0214-0.1114129.4019200.306547.5351
52.24730.00450.63682.0487-0.19021.53640.04830.0829-0.2027-0.12180.02220.21530.2742-0.1136-0.0705-0.0835-0.05440.0343-0.12780.0136-0.079498.8414162.873651.132
60.81910.02690.11511.3498-0.43411.9796-0.0285-0.0034-0.1021-0.07810.03890.20820.0223-0.1557-0.0104-0.1621-0.01480.0002-0.1583-0.0061-0.110598.7723173.995347.386
71.9730.1051-0.72351.8535-0.27771.66790.029-0.02860.25370.14860.03970.2353-0.2251-0.1493-0.0688-0.09010.0377-0.047-0.13940.0152-0.028997.9023210.923744.7591
80.70250.0536-0.30951.5465-0.43411.769-0.01880.0410.10030.09420.05170.214-0.0203-0.1796-0.0329-0.16240.0216-0.0157-0.1453-0.0109-0.102798.3414199.812948.5004
92.4475-0.5-0.09692.22130.29181.796-0.10020.26670.1647-0.35130.0290.2265-0.2284-0.21090.0712-0.0064-0.0548-0.1028-0.04750.0002-0.114860.6948136.132370.5805
100.71-0.0672-0.02151.86470.53421.4504-0.04030.09290.0096-0.12920.00380.2195-0.0721-0.2380.0366-0.113-0.0238-0.0649-0.09870.0216-0.129561.4448140.00881.6408
111.83960.27060.43342.20290.13941.53010.067-0.2706-0.01450.2741-0.0350.21550.0353-0.1286-0.0321-0.11330.04610.0305-0.0622-0.0132-0.134662.8413143.0244118.4923
120.77130.2608-0.13261.89160.31141.55-0.0461-0.08710.0424-0.04480.03060.17770.0469-0.16750.0155-0.19370.0172-0.0108-0.12060.0158-0.138862.5587139.1632107.4235
132.0324-0.84190.18782.0046-0.3051.35710.03460.2198-0.059-0.3313-0.0071-0.09710.10450.099-0.0275-0.0535-0.050.028-0.10660.0065-0.160592.1822143.830969.4623
140.6611-0.1530.0681.8301-0.4971.3314-0.00360.05380.0313-0.10450.0169-0.09360.09030.1391-0.0133-0.1291-0.0110.015-0.146-0.013-0.168592.4033139.380980.3092
152.61940.89290.13891.8814-0.05461.85080.0123-0.23390.06990.2465-0.011-0.187-0.07240.1517-0.0013-0.1310.0501-0.0454-0.1102-0.0076-0.132194.2055134.2822116.9189
160.65620.21650.07871.6788-0.34931.3908-0.0447-0.0867-0.0041-0.03390.0319-0.1208-0.0360.13740.0128-0.18640.0197-0.0113-0.1267-0.0247-0.157193.6228138.7582106.1132
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 651 - 61
22AA69 - 22563 - 219
33BB5 - 651 - 61
44BB69 - 22563 - 219
55CC5 - 651 - 61
66CC69 - 22563 - 219
77DD5 - 651 - 61
88DD69 - 22563 - 219
99EE5 - 651 - 61
1010EE69 - 22563 - 219
1111FF5 - 651 - 61
1212FF69 - 22563 - 219
1313GG5 - 651 - 61
1414GG69 - 22563 - 219
1515HH5 - 651 - 61
1616HH69 - 22563 - 219

+
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