[English] 日本語
Yorodumi
- PDB-5ma8: GFP-binding DARPin 3G124nc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ma8
TitleGFP-binding DARPin 3G124nc
Components
  • GA-binding protein subunit beta-1
  • Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / green fluorescent protein / designed ankyrin protein
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / protein-chromophore linkage / Green fluorescent protein
Function and homology information
Biological speciessynthetic construct (others)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHansen, S. / Stueber, J. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Plueckthun, A.
CitationJournal: Sci Rep / Year: 2017
Title: Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity.
Authors: Hansen, S. / Stuber, J.C. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Pluckthun, A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GA-binding protein subunit beta-1
C: GA-binding protein subunit beta-1
B: Green fluorescent protein
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)88,8384
Polymers88,8384
Non-polymers00
Water3,261181
1
A: GA-binding protein subunit beta-1
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)44,4192
Polymers44,4192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-11 kcal/mol
Surface area16250 Å2
MethodPISA
2
C: GA-binding protein subunit beta-1
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)44,4192
Polymers44,4192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-10 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)62.140, 62.140, 213.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein/peptide GA-binding protein subunit beta-1


Mass: 16965.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Protein/peptide Green fluorescent protein /


Mass: 27453.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P42212
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.3 M Sodium Acetate. 0.1M TRIS (HOAc) pH 7.5, 25% PEG 2K MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.35→43.94 Å / Num. obs: 33548 / % possible obs: 99.9 % / Redundancy: 13.9 % / Net I/σ(I): 22.33

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→43.94 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1657 4.95 %
Rwork0.1894 --
Obs0.1916 33484 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 0 181 6147
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0046093
f_angle_d0.898254
f_dihedral_angle_d15.2122204
f_chiral_restr0.034920
f_plane_restr0.0041084
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3501-2.41930.361230.29722688100
2.4193-2.49740.33311340.2822663100
2.4974-2.58660.30391580.27112647100
2.5866-2.69020.28761510.25182620100
2.6902-2.81260.2861500.22972621100
2.8126-2.96080.26861500.2315265599
2.9608-3.14630.28491460.22472604100
3.1463-3.38910.26841210.20272674100
3.3891-3.730.24891260.18832646100
3.73-4.26940.20071260.16232666100
4.2694-5.37740.18681160.14322681100
5.3774-43.94730.17481560.1492662100
Refinement TLS params.

Method: refined / Refinement-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)
13.00240.6423-0.11061.9627-0.17653.9290.1852-0.01120.73490.5882-0.5320.0451-0.52440.68660.03980.3864-0.04990.04780.4966-0.04990.8702-79.444552.849522.5334
21.6504-0.9492-0.07020.91980.51031.2583-0.0445-0.17281.09330.2381-0.2030.63170.0498-0.0568-0.06390.3202-0.03720.10070.46840.01630.9033-83.233349.983619.8444
30.5315-0.5521-0.03162.1377-0.60982.41930.21720.21210.16080.39010.03980.7884-0.13280.0531-0.02250.292-0.020.06830.3938-0.03580.6657-81.783140.838421.2251
40.955-0.27590.17480.72310.19350.80970.13440.3530.2659-0.0024-0.09330.38290.12670.0642-0.02710.24990.0343-0.00120.53870.04420.4826-76.918236.388716.0387
50.84360.6378-0.06621.2515-0.05990.99780.12830.5509-0.0009-0.294-0.0226-0.04810.27810.0797-0.00770.28480.073-0.03840.63590.03170.4425-70.64232.76849.6178
60.4976-0.3334-0.69771.6632-1.51063.7959-0.1586-0.3829-0.2630.04050.1833-0.74710.97480.48060.02080.38170.1467-0.05650.6502-0.0140.4311-67.382627.169618.8568
70.6968-0.10050.82921.40570.08521.1145-0.37770.019-0.47880.70550.38330.19180.6583-0.6605-0.00080.4790.0853-0.03190.5207-0.06070.5713-76.147221.994318.2412
82.86251.00280.01380.7946-0.10680.96730.097-0.17410.0332-0.188-0.0746-0.15260.18560.2159-0.01250.35090.12560.0050.6715-0.07510.4067-65.283925.33628.899
90.1140.1866-0.54940.3259-0.91852.83960.0554-0.12560.21460.0012-0.3636-0.41970.12410.54410.01510.47560.1709-0.03320.53690.09480.5892-60.944921.260918.601
101.41520.67930.2162.33631.51743.96530.05990.2291-1.03040.26-0.50960.1560.79980.2018-0.04090.52920.05360.04560.5542-0.06980.7244-67.62514.41617.5412
111.86710.2993-0.62713.4418-2.0954.59930.16610.25780.2001-0.83950.08340.18520.41390.0164-0.03880.46990.06420.01710.5104-0.13260.5846-24.420979.5425-16.8896
122.76651.6828-2.17663.4231-1.91751.95640.0538-0.3763-0.416-0.2758-0.3561-0.91410.67280.98560.04830.47030.15440.01170.7694-0.09360.6925-16.954974.2487-12.9618
131.8532-0.116-0.62231.4514-0.16361.47560.0468-0.0940.2377-0.04510.1475-0.39110.19650.24020.00310.33580.00920.01720.5162-0.13310.5001-23.978280.5547-7.696
140.95260.1394-0.38661.0246-0.22551.20330.0944-0.45650.20710.04260.0672-0.19470.07340.1889-0.00520.3208-0.03640.0120.5238-0.11680.4609-30.008383.63981.8986
150.63890.3657-0.84342.74820.04781.27260.0554-0.7505-0.39610.5345-0.1649-0.03520.3626-0.2875-0.07920.4827-0.08930.01530.73330.02530.4985-34.599277.719711.2669
161.304-0.7069-0.24180.821-0.03090.498-0.2255-0.3292-0.09730.22310.26680.01020.171-0.136-0.02080.3269-0.05310.02330.6807-0.14960.4734-40.296987.860811.8474
171.15270.8706-0.37252.4285-1.25560.642-0.0332-0.446-0.7207-0.10970.53690.7438-0.0615-0.187-0.02390.4076-0.13110.03970.63950.11870.5652-45.491777.914613.3622
182.98110.740.20082.8477-0.20083.3720.3734-0.5094-0.66760.9125-0.25740.3050.1459-0.17430.00440.61250.038-0.01151.02140.09410.5921-39.872276.198420.7193
190.82670.65490.55010.6080.6440.88830.2709-0.8888-0.42540.7327-0.40790.22030.40530.3182-0.03690.4825-0.04110.02350.7901-0.03210.6264-60.818840.231935.7003
202.96260.7182-0.82480.1986-0.28291.14220.0049-0.1651.15350.0537-0.1938-0.3676-0.23130.06-0.74180.397-0.00810.15890.46150.00171.4609-49.84854.243318.873
210.2399-0.3872-0.0510.5195-0.17832.0379-0.1531-0.06551.0996-0.14440.2016-0.11960.032-0.34110.05980.25320.0330.03260.44570.08870.9058-57.187248.597717.9457
221.0568-1.4985-0.4112.50910.54051.0483-0.21640.32830.5289-0.6903-0.5170.4441-0.4341-0.3278-0.00560.41480.09670.16840.54650.1221.156-49.173356.1747.6973
230.17490.1561-0.04980.4686-0.0820.45060.26540.15660.7754-0.1167-0.10190.1233-0.190.12690.05010.270.01320.06850.53760.13540.9493-49.045747.015113.3705
242.1165-0.5135-0.43761.1627-0.23282.20590.0146-0.09031.01290.13580.2884-0.36990.31960.04010.38420.07170.02310.05270.4368-0.0760.7846-46.852644.266620.7944
250.86690.0387-0.42211.7942-0.24252.5669-0.2552-0.12540.54680.05190.0251-0.63090.18260.41390.05970.23230.0517-0.02710.5512-0.03030.5707-41.719536.583619.6827
261.3833-0.4033-0.35770.75110.2321.5267-0.0550.07240.40790.06940.1001-0.13910.11140.05290.02880.22350.0160.01230.46270.03750.5011-50.663240.255720.1366
270.68470.92850.99411.24781.36821.9991-0.4419-0.3279-0.7190.46310.13410.04470.99590.1782-0.01640.4790.04430.07340.4347-0.09011.1456-45.532665.6652-9.0017
283.3808-1.95490.53643.0635-0.37970.02220.09391.626-0.0678-0.6077-0.22290.0530.0234-0.49960.12630.42020.2149-0.08591.1439-0.09650.4131-53.020486.3363-19.8126
290.9693-0.57370.09662.2269-0.46790.6007-0.08870.73670.0395-0.3479-0.1946-0.3457-0.2548-0.317-0.02190.46960.16160.00250.75210.07480.3919-49.043287.3832-17.938
301.675-0.3923-0.00230.83970.47361.1770.44810.7545-0.4655-0.2935-0.16590.01090.1264-0.05060.00570.33890.09830.04420.42940.04070.4372-44.098282.7108-9.1237
311.1877-0.1992-0.5990.7995-0.38520.81440.40890.11390.0703-0.2290.06620.127-0.07510.6482-0.05670.45370.12010.0371.01230.17140.5926-52.498397.6049-19.1996
321.51940.5703-3.02581.225-1.5186.16490.50091.30190.4683-0.5979-0.2490.32080.4088-0.3368-0.09450.37670.2216-0.07160.75450.0290.5037-54.393589.8593-11.6507
331.7354-0.7832.29442.0041-0.80013.0914-0.46350.378-1.83590.3362-0.07680.89660.53320.0021-0.05170.54440.0270.23870.4196-0.04491.0371-52.46569.9772-1.0816
340.13930.33440.16181.6462-0.18251.43320.01911.0714-1.44250.0276-0.13680.7752-0.3071-0.65310.44530.04170.0911-0.21920.9327-0.57821.4276-60.761678.7853-11.4282
351.1406-0.72230.14152.14430.53650.8421-0.0815-0.0377-0.136-0.61810.27770.2876-0.1405-0.71631.07790.29480.0376-0.52551.2105-0.71170.6838-59.23380.4846-17.8823
360.57630.6728-0.22470.7142-0.20720.53460.39551.1976-0.113-0.7738-0.4480.3196-0.3233-0.40080.00250.67610.2653-0.12480.9877-0.18790.5611-58.425489.6433-17.3095
370.59070.40810.72990.33380.58881.05460.34880.24540.424-0.0411-0.1464-0.0131-0.2573-0.90430.07710.33310.15670.12970.35060.07810.5958-54.431395.7216-3.8876
380.20730.62150.43342.21480.84461.24460.20960.5331-0.9302-0.47590.08410.4922-0.1267-0.4764-0.00960.4732-0.05810.02330.6427-0.17721.3793-66.290872.2945-5.4913
391.93950.6027-0.58360.3221-0.12095.06040.37040.8861-0.88890.4452-0.07240.4056-0.6136-0.72130.83740.0347-0.0209-0.02320.6091-0.25840.9434-62.947787.0792-4.9388
400.3103-0.1014-0.13570.6169-0.98411.80340.28220.2591-0.2985-0.03290.47790.81020.47750.1270.42990.6743-0.20420.25850.3991-0.50691.8137-61.497764.8082-9.2562
412.0911-1.027-1.04812.61620.15711.09140.05810.15520.0933-0.05250.03770.3987-0.1305-0.0749-0.00020.26060.0270.04970.38730.07430.5166-47.610186.8369-5.7399
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11chain 'A' and (resid 13 through 24 )
22chain 'A' and (resid 25 through 49 )
33chain 'A' and (resid 50 through 68 )
44chain 'A' and (resid 69 through 101 )
55chain 'A' and (resid 102 through 115 )
66chain 'A' and (resid 116 through 125 )
77chain 'A' and (resid 126 through 134 )
88chain 'A' and (resid 135 through 148 )
99chain 'A' and (resid 149 through 158 )
1010chain 'A' and (resid 159 through 169 )
1111chain 'C' and (resid 11 through 24 )
1212chain 'C' and (resid 25 through 35 )
1313chain 'C' and (resid 36 through 68 )
1414chain 'C' and (resid 69 through 115 )
1515chain 'C' and (resid 116 through 134 )
1616chain 'C' and (resid 135 through 148 )
1717chain 'C' and (resid 149 through 158 )
1818chain 'C' and (resid 159 through 168 )
1919chain 'B' and (resid 3 through 11 )
2020chain 'B' and (resid 12 through 24 )
2121chain 'B' and (resid 25 through 48 )
2222chain 'B' and (resid 49 through 56 )
2323chain 'B' and (resid 57 through 64 )
2424chain 'B' and (resid 68 through 148 )
2525chain 'B' and (resid 149 through 175 )
2626chain 'B' and (resid 176 through 230 )
2727chain 'D' and (resid 3 through 11 )
2828chain 'D' and (resid 12 through 24 )
2929chain 'D' and (resid 25 through 36 )
3030chain 'D' and (resid 37 through 48 )
3131chain 'D' and (resid 49 through 56 )
3232chain 'D' and (resid 57 through 64 )
3333chain 'D' and (resid 68 through 81 )
3434chain 'D' and (resid 82 through 104 )
3535chain 'D' and (resid 105 through 114 )
3636chain 'D' and (resid 115 through 138 )
3737chain 'D' and (resid 139 through 148 )
3838chain 'D' and (resid 149 through 159 )
3939chain 'D' and (resid 160 through 187 )
4040chain 'D' and (resid 188 through 198 )
4141chain 'D' and (resid 199 through 229 )

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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