[English] 日本語
Yorodumi
- PDB-4h3m: mPlumAYC-E16A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h3m
TitlemPlumAYC-E16A
ComponentsFluorescent protein plumFluorescence
KeywordsFLUORESCENT PROTEIN
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
Fluorescent protein plum
Similarity search - Component
Biological speciesDiscosoma sp. LW-2004 (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMoore, M.M. / Chica, R.A.
CitationJournal: Plos One / Year: 2012
Title: Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design.
Authors: Moore, M.M. / Oteng-Pabi, S.K. / Pandelieva, A.T. / Mayo, S.L. / Chica, R.A.
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Sep 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_conn / struct_ref_seq_dif
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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fluorescent protein plum
B: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)53,0842
Polymers53,0842
Non-polymers00
Water3,801211
1
A: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)26,5421
Polymers26,5421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)26,5421
Polymers26,5421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.240, 64.690, 94.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 6:64 or resseq 69:204 or resseq 208:220 )
211chain 'B' and (resseq 6:64 or resseq 69:204 or resseq 208:220 )

-
Components

#1: Protein Fluorescent protein plum / Fluorescence / mPlumAYC-E16A


Mass: 26541.914 Da / Num. of mol.: 2 / Mutation: E16A,T195A,I197Y,A217C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S3G7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET66, TYR67, AND GLY68 CIRCULARIZED INTO ONE CHROMOPHORE (NRQ).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.3 uL + 0.3 uL drops, precipitant: 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, 50% (v/v) PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.5418, 1.5621, 1.7321
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.56211
31.73211
ReflectionResolution: 2→53.429 Å / Num. all: 26118 / Num. obs: 23844 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.112.60.154.4195.1
2.24-2.39194.2
2.58-2.83194.3
3.16-3.65191.9
4.47-6.32185.5

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QLG
Resolution: 2→40.26 Å / SU ML: 0.28 / σ(F): 1.38 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 1206 5.07 %RANDOM
Rwork0.2148 ---
obs0.2178 23808 91.17 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.282 Å2 / ksol: 0.438 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7892 Å20 Å2-0 Å2
2--6.1624 Å20 Å2
3----0.8828 Å2
Refinement stepCycle: LAST / Resolution: 2→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 0 211 3396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013362
X-RAY DIFFRACTIONf_angle_d1.3974581
X-RAY DIFFRACTIONf_dihedral_angle_d13.9921187
X-RAY DIFFRACTIONf_chiral_restr0.083487
X-RAY DIFFRACTIONf_plane_restr0.005605
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1450X-RAY DIFFRACTIONPOSITIONAL
12B1450X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.33241260.21632575X-RAY DIFFRACTION95
2.0801-2.17480.28121390.19622526X-RAY DIFFRACTION93
2.1748-2.28940.29071610.21112410X-RAY DIFFRACTION90
2.2894-2.43290.28731260.20712608X-RAY DIFFRACTION95
2.4329-2.62070.29321240.21622521X-RAY DIFFRACTION92
2.6207-2.88430.32981480.20922458X-RAY DIFFRACTION90
2.8843-3.30150.24231270.21422567X-RAY DIFFRACTION93
3.3015-4.15890.22661270.19782487X-RAY DIFFRACTION89
4.1589-40.26840.26751280.252450X-RAY DIFFRACTION84
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.31360.23540.19070.2360.04450.2834-0.01050.0743-0.0733-0.03140.0268-0.07430.01550.0536-0.07970.03680.00110.06540.1156-0.1470.1586-18.7464-21.3027-5.9755
20.2067-0.13930.25230.37010.47351.8502-0.1041-0.127-0.01820.14080.09980.02270.07830.0734-0.12990.05020.05290.01020.05030.04340.0314-19.0532-20.913417.4881
30.8453-0.3125-0.49481.57861.08821.7525-0.0694-0.0474-0.04230.13110.02770.02260.17360.1390.02670.09520.06690.07580.0790.06440.0235-20.667-23.595222.6596
40.09630.04360.10470.0744-0.05540.6485-0.01490.037-0.0091-0.0356-0.02210.01910.0022-0.0462-0.05510.0282-0.0344-0.02230.0673-0.0636-0.0527-23.6408-18.61190.9423
52.76061.1458-1.28641.3127-1.03611.28310.00080.10630.0911-0.05760.07520.05310.0358-0.06530.03960.0167-0.018-0.04410.09190.06490.1283-24.8866-14.01082.0526
60.10180.158-0.04130.2639-0.08530.03080.0484-0.0913-0.00340.0773-0.00180.0305-0.05020.0170.11130.0017-0.0410.05390.09360.10040.0345-26.7722-21.4121.8555
70.11170.197-0.00460.49110.31620.7199-0.0619-0.0586-0.0305-0.06250.0836-0.0781-0.03560.0358-0.00330.01540.0264-0.01390.0499-0.00660.0234-20.623-12.966414.1491
80.50820.00650.08290.2705-0.06830.42580.09160.0649-0.0359-0.05030.0387-0.0092-0.0030.01580.21980.01890.04810.0241-0.09780.00340.1102-10.2919-13.4137-1.9134
90.7311-0.6357-0.80641.84811.43292.0405-0.0318-0.1590.16720.1010.1093-0.053-0.09310.0351-0.04430.04480.04090.00610.0724-0.0980.1002-12.1749-7.780519.3062
100.3309-0.331-0.33770.7680.62240.532-0.0827-0.12290.10210.13150.110.0099-0.00660.02070.03220.09510.069-0.02590.0651-0.01150.0608-11.6706-12.253120.8211
110.3063-0.4679-0.26771.10480.23990.30790.05410.0525-0.0679-0.01430.00720.04550.0670.0075-0.04580.15440.0853-0.07890.0417-0.04580.1828-12.4637-25.41044.6893
120.5707-0.23320.09330.304-0.28710.3085-0.046-0.132-0.03290.06180.03040.0542-0.04820.0003-0.1130.06940.04730.02470.05020.02650.0798-15.5047-19.956814.1611
131.0037-0.2752-0.03780.1131-0.05060.1022-0.0669-0.12130.08190.11620.0787-0.0292-0.0692-0.00840.08910.16870.1187-0.02780.1194-0.02690.0587-22.8687-6.359431.6432
140.16150.0508-0.07520.1105-0.21730.4245-0.01250.01010.00750.05620.02660.0261-0.0642-0.0691-0.08550.06090.1943-0.01180.13130.00750.0621-25.9246-3.418417.3209
150.3286-0.0723-0.11480.24910.04290.1317-0.0423-0.02270.05460.10560.0180.0567-0.0935-0.0362-0.0765-0.02920.11480.0279-0.1042-0.0460.0557-11.1708-3.143310.9425
160.01450.0566-0.04080.35570.04330.44250.0425-0.04580.09950.11040.030.1462-0.1245-0.09740.2487-0.02430.13740.08810.0771-0.1380.1009-17.597-2.579118.2687
170.3948-0.1723-0.07640.7151-0.00380.2289-0.02050.00980.0170.0096-0.00610.0451-0.079-0.0806-0.00950.04450.03310.00840.0243-0.00150.0615-5.0061-10.20851.1776
180.6690.3053-0.38280.6589-0.19540.3746-0.0628-0.0105-0.04880.0352-0.01520.03170.0551-0.0345-0.14240.0460.05350.06610.0043-0.03780.0639-26.2965-8.14139.6401
190.9090.6551-0.85210.7139-0.61362.52490.0666-0.1134-0.01520.1987-0.02070.1142-0.0204-0.0673-0.10030.11250.01650.08070.09470.10840.0822-33.1526-17.768219.4289
200.94251.2192-0.77881.6553-0.84362.0978-0.02280.052-0.0023-0.0623-0.00390.15650.1779-0.1338-0.05690.06010.03250.00740.05890.0130.0855-21.7007-6.92693.5059
211.0276-0.56070.57091.7586-0.08012.4963-0.0073-0.1286-0.09430.158-0.05790.09440.157-0.08030.06790.071-0.01840.04290.12640.05670.0863.7226-21.37352.8869
220.0313-0.04170.03280.1063-0.03120.2835-0.00220.0188-0.0206-0.03980.0128-0.03790.08310.0026-0.03930.09710.0001-0.0346-0.0282-0.03430.09495.1983-23.09137.8455
231.3687-1.08890.0171.07250.70742.51160.01090.0507-0.1053-0.0313-0.00560.04960.1204-0.04010.00010.1568-0.0869-0.09090.1388-0.0530.09433.5191-17.751817.0363
240.32430.01140.43970.35070.35384.61730.0068-0.0227-0.10380.07430.089-0.03430.28020.1234-0.21450.1330.0232-0.05380.1045-0.04470.10048.2948-23.478631.8982
253.5996-0.7953-0.86392.15930.0360.2202-0.0067-0.33610.11240.09430.0237-0.1789-0.00030.124-0.02690.03180.0321-0.01090.13590.00660.0557.9291-14.77651.3938
260.22330.20040.08560.7558-0.17940.2840.07020.2264-0.0474-0.21390.12230.03140.02660.11210.17980.06530.0185-0.00610.1557-0.03470.0338.581-15.928532.3294
270.4822-0.02420.03140.0853-0.13810.2262-0.0251-0.0664-0.0030.01970.0338-0.0397-0.0198-0.0290.01220.02410.02750.0101-0.036-0.04580.0828-3.9477-13.06249.4132
281.27590.4173-1.01532.3643-2.45572.83850.06810.1920.0712-0.22540.07370.0624-0.0985-0.0034-0.04650.149-0.0377-0.00050.16030.04320.0598-2.1576-7.980428.4903
290.46230.1299-0.42290.19750.12370.7510.03550.11720.0809-0.06950.10280.0369-0.0201-0.05550.18550.0306-0.0327-0.0070.11510.03750.0016-3.0424-12.472926.9637
301.039-0.527-0.05275.2534-2.15241.306-0.0365-0.0103-0.0851-0.04160.02870.0320.0555-0.029-0.10510.1968-0.0425-0.01450.05610.02260.0857-2.1445-25.856742.7788
310.46960.1731-0.04360.4154-0.24120.66910.02360.1491-0.0095-0.11760.07350.06750.0568-0.02190.04650.0808-0.0369-0.02580.0699-0.02430.02930.807-18.199531.0804
321.27320.551.78531.06831.28133.4554-0.07220.17930.0318-0.08860.0562-0.0281-0.11690.16770.04090.1596-0.1047-0.03450.2805-0.01950.06159.2033-6.654815.2051
330.89840.219-0.48280.1651-0.33220.66490.02450.06880.04150.0598-0.0235-0.0313-0.17960.1543-0.11520.1327-0.0865-0.00590.1781-0.00270.02718.6005-3.987931.6011
341.37261.1306-1.56372.0269-0.9932.0133-0.01970.18860.054-0.12010.06340.1024-0.0734-0.3065-0.03180.10990.02920.01970.12130.00980.0619-9.4857-4.776639.8536
355.9546-0.7692-2.40622.5477-0.18633.16930.07880.02480.1676-0.0629-0.0635-0.1862-0.08550.0807-0.06540.2248-0.13730.03180.13630.03950.079710.2675-0.861727.7674
360.40490.2208-0.68731.0307-0.20991.2180.04410.1070.1496-0.1346-0.0004-0.1507-0.24990.0882-0.0970.0918-0.07090.03030.19220.13680.13271.7575-2.943430.047
370.7010.5324-0.11731.92830.05020.3038-0.05920.0668-0.01360.0150.04590.1020.0449-0.195-0.01230.1036-0.00310.02220.09270.0180.0503-10.4027-11.033346.7668
386.455-3.9959-4.04162.87992.82423.2715-0.0246-0.0390.15240.0603-0.0271-0.0338-0.1250.1099-0.04480.1268-0.03680.04020.08490.00120.08579.4758-6.637939.1879
392.6132-0.4656-1.12641.59090.05352.21490.1020.2745-0.0221-0.24820.0344-0.11740.00290.1039-0.07740.10660.03150.05470.2366-0.0210.083116.3754-16.491632.9703
401.1203-0.0218-0.92180.44580.08012.1490.06140.02060.24070.1096-0.00340.1832-0.3302-0.0440.03850.1704-0.0204-0.00020.0808-0.04950.26323.6818-3.161246.7644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:11)
2X-RAY DIFFRACTION2(chain A and resid 12:25)
3X-RAY DIFFRACTION3(chain A and resid 26:30)
4X-RAY DIFFRACTION4(chain A and resid 31:38)
5X-RAY DIFFRACTION5(chain A and resid 39:44)
6X-RAY DIFFRACTION6(chain A and resid 45:55)
7X-RAY DIFFRACTION7(chain A and resid 56:72)
8X-RAY DIFFRACTION8(chain A and resid 73:91)
9X-RAY DIFFRACTION9(chain A and resid 92:101)
10X-RAY DIFFRACTION10(chain A and resid 102:109)
11X-RAY DIFFRACTION11(chain A and resid 110:115)
12X-RAY DIFFRACTION12(chain A and resid 116:128)
13X-RAY DIFFRACTION13(chain A and resid 129:138)
14X-RAY DIFFRACTION14(chain A and resid 139:146)
15X-RAY DIFFRACTION15(chain A and resid 147:167)
16X-RAY DIFFRACTION16(chain A and resid 168:181)
17X-RAY DIFFRACTION17(chain A and resid 182:195)
18X-RAY DIFFRACTION18(chain A and resid 196:203)
19X-RAY DIFFRACTION19(chain A and resid 204:212)
20X-RAY DIFFRACTION20(chain A and resid 213:220)
21X-RAY DIFFRACTION21(chain B and resid 6:11)
22X-RAY DIFFRACTION22(chain B and resid 12:20)
23X-RAY DIFFRACTION23(chain B and resid 21:26)
24X-RAY DIFFRACTION24(chain B and resid 27:34)
25X-RAY DIFFRACTION25(chain B and resid 35:39)
26X-RAY DIFFRACTION26(chain B and resid 40:72)
27X-RAY DIFFRACTION27(chain B and resid 73:91)
28X-RAY DIFFRACTION28(chain B and resid 92:101)
29X-RAY DIFFRACTION29(chain B and resid 102:109)
30X-RAY DIFFRACTION30(chain B and resid 110:115)
31X-RAY DIFFRACTION31(chain B and resid 116:129)
32X-RAY DIFFRACTION32(chain B and resid 130:137)
33X-RAY DIFFRACTION33(chain B and resid 138:149)
34X-RAY DIFFRACTION34(chain B and resid 150:161)
35X-RAY DIFFRACTION35(chain B and resid 162:169)
36X-RAY DIFFRACTION36(chain B and resid 170:181)
37X-RAY DIFFRACTION37(chain B and resid 182:193)
38X-RAY DIFFRACTION38(chain B and resid 194:202)
39X-RAY DIFFRACTION39(chain B and resid 203:214)
40X-RAY DIFFRACTION40(chain B and resid 215:222)

+
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