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- PDB-5ma8: GFP-binding DARPin 3G124nc -

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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 / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Beta Barrel ...Ankyrin repeat-containing domain / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
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.
History
DepositionNov 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
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

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Components

#1: Protein 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 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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046093
X-RAY DIFFRACTIONf_angle_d0.898254
X-RAY DIFFRACTIONf_dihedral_angle_d15.2122204
X-RAY DIFFRACTIONf_chiral_restr0.034920
X-RAY DIFFRACTIONf_plane_restr0.0041084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.41930.361230.29722688X-RAY DIFFRACTION100
2.4193-2.49740.33311340.2822663X-RAY DIFFRACTION100
2.4974-2.58660.30391580.27112647X-RAY DIFFRACTION100
2.5866-2.69020.28761510.25182620X-RAY DIFFRACTION100
2.6902-2.81260.2861500.22972621X-RAY DIFFRACTION100
2.8126-2.96080.26861500.23152655X-RAY DIFFRACTION99
2.9608-3.14630.28491460.22472604X-RAY DIFFRACTION100
3.1463-3.38910.26841210.20272674X-RAY DIFFRACTION100
3.3891-3.730.24891260.18832646X-RAY DIFFRACTION100
3.73-4.26940.20071260.16232666X-RAY DIFFRACTION100
4.2694-5.37740.18681160.14322681X-RAY DIFFRACTION100
5.3774-43.94730.17481560.1492662X-RAY DIFFRACTION100
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)
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
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 115 )
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 125 )
7X-RAY DIFFRACTION7chain 'A' and (resid 126 through 134 )
8X-RAY DIFFRACTION8chain 'A' and (resid 135 through 148 )
9X-RAY DIFFRACTION9chain 'A' and (resid 149 through 158 )
10X-RAY DIFFRACTION10chain 'A' and (resid 159 through 169 )
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 24 )
12X-RAY DIFFRACTION12chain 'C' and (resid 25 through 35 )
13X-RAY DIFFRACTION13chain 'C' and (resid 36 through 68 )
14X-RAY DIFFRACTION14chain 'C' and (resid 69 through 115 )
15X-RAY DIFFRACTION15chain 'C' and (resid 116 through 134 )
16X-RAY DIFFRACTION16chain 'C' and (resid 135 through 148 )
17X-RAY DIFFRACTION17chain 'C' and (resid 149 through 158 )
18X-RAY DIFFRACTION18chain 'C' and (resid 159 through 168 )
19X-RAY DIFFRACTION19chain 'B' and (resid 3 through 11 )
20X-RAY DIFFRACTION20chain 'B' and (resid 12 through 24 )
21X-RAY DIFFRACTION21chain 'B' and (resid 25 through 48 )
22X-RAY DIFFRACTION22chain 'B' and (resid 49 through 56 )
23X-RAY DIFFRACTION23chain 'B' and (resid 57 through 64 )
24X-RAY DIFFRACTION24chain 'B' and (resid 68 through 148 )
25X-RAY DIFFRACTION25chain 'B' and (resid 149 through 175 )
26X-RAY DIFFRACTION26chain 'B' and (resid 176 through 230 )
27X-RAY DIFFRACTION27chain 'D' and (resid 3 through 11 )
28X-RAY DIFFRACTION28chain 'D' and (resid 12 through 24 )
29X-RAY DIFFRACTION29chain 'D' and (resid 25 through 36 )
30X-RAY DIFFRACTION30chain 'D' and (resid 37 through 48 )
31X-RAY DIFFRACTION31chain 'D' and (resid 49 through 56 )
32X-RAY DIFFRACTION32chain 'D' and (resid 57 through 64 )
33X-RAY DIFFRACTION33chain 'D' and (resid 68 through 81 )
34X-RAY DIFFRACTION34chain 'D' and (resid 82 through 104 )
35X-RAY DIFFRACTION35chain 'D' and (resid 105 through 114 )
36X-RAY DIFFRACTION36chain 'D' and (resid 115 through 138 )
37X-RAY DIFFRACTION37chain 'D' and (resid 139 through 148 )
38X-RAY DIFFRACTION38chain 'D' and (resid 149 through 159 )
39X-RAY DIFFRACTION39chain 'D' and (resid 160 through 187 )
40X-RAY DIFFRACTION40chain 'D' and (resid 188 through 198 )
41X-RAY DIFFRACTION41chain 'D' and (resid 199 through 229 )

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  • 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

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