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- PDB-5j7k: Loop grafting onto a highly stable FN3 scaffold -

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Open data


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Basic information

Entry
Database: PDB / ID: 5j7k
TitleLoop grafting onto a highly stable FN3 scaffold
ComponentsFN3con-a-lys
KeywordsPROTEIN BINDING / loop grafting / rational design / fibronectin type III / FN3 / protein binding-hydrolase complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsPorebski, B.T. / Drinkwater, N. / McGowan, S. / Buckle, A.M.
CitationJournal: Protein Eng.Des.Sel. / Year: 2016
Title: Circumventing the stability-function trade-off in an engineered FN3 domain.
Authors: Porebski, B.T. / Conroy, P.J. / Drinkwater, N. / Schofield, P. / Vazquez-Lombardi, R. / Hunter, M.R. / Hoke, D.E. / Christ, D. / McGowan, S. / Buckle, A.M.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FN3con-a-lys
B: FN3con-a-lys
C: FN3con-a-lys
D: FN3con-a-lys
E: FN3con-a-lys
F: FN3con-a-lys
G: FN3con-a-lys
H: FN3con-a-lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,07615
Polymers88,6188
Non-polymers4587
Water1,24369
1
A: FN3con-a-lys
C: FN3con-a-lys
E: FN3con-a-lys
H: FN3con-a-lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5057
Polymers44,3094
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FN3con-a-lys
D: FN3con-a-lys
F: FN3con-a-lys
G: FN3con-a-lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5718
Polymers44,3094
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.220, 71.230, 126.141
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FN3con-a-lys


Mass: 11077.237 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 61.98 % / Description: Large flat plates that formed within 2 days.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5% glycerol, 10% 2-propanol, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.46→50.22 Å / Num. obs: 32118 / % possible obs: 98.8 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.6
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.7 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U3H
Resolution: 2.46→50.219 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.28 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2854 1630 5.08 %Random selection
Rwork0.2594 ---
obs0.2611 32099 98.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→50.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4338 0 7 69 4414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054437
X-RAY DIFFRACTIONf_angle_d1.0586075
X-RAY DIFFRACTIONf_dihedral_angle_d15.0442485
X-RAY DIFFRACTIONf_chiral_restr0.057726
X-RAY DIFFRACTIONf_plane_restr0.007756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.53940.33651340.35642749X-RAY DIFFRACTION94
2.5394-2.63020.32581370.35282790X-RAY DIFFRACTION94
2.6302-2.73550.34821510.32392743X-RAY DIFFRACTION94
2.7355-2.860.36051460.31822732X-RAY DIFFRACTION94
2.86-3.01070.32911590.28742786X-RAY DIFFRACTION94
3.0107-3.19930.31671390.27742745X-RAY DIFFRACTION94
3.1993-3.44620.32881360.25512797X-RAY DIFFRACTION94
3.4462-3.79280.30951690.2552776X-RAY DIFFRACTION93
3.7928-4.34110.2411490.22772768X-RAY DIFFRACTION94
4.3411-5.46750.21471550.19882817X-RAY DIFFRACTION94
5.4675-42.05190.29031320.27792786X-RAY DIFFRACTION92
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)
14.99691.10072.21585.18342.69881.9680.047-0.53520.07310.5348-0.00650.0713-0.1463-0.00890.02490.4559-0.0031-0.070.29470.07160.344890.808516.2156129.4068
20.4555-1.2404-0.623.4692.64792.00090.05020.0220.21010.1890.2498-0.3723-0.41380.3257-0.15340.4859-0.01520.07160.28230.08240.484992.040314.1703114.8436
30.42640.4137-0.10332.3298-0.39292.0004-0.1922-0.08580.3728-0.2954-0.227-0.2855-0.70890.29640.2321-0.1314-0.0681-0.01090.35910.09450.584294.040312.1162124.7824
43.2329-6.72691.90162.0008-3.97841.139-0.1845-0.541-0.09740.67770.2224-0.5553-0.08250.2318-0.0610.5-0.1804-0.0690.77520.02930.461797.86728.4102137.6201
56.9688-1.03644.74951.7045-0.97735.1487-0.068-0.0472-0.22080.49850.31560.26350.23530.1694-0.16790.5248-0.05160.05910.46910.07660.310188.13883.505125.5898
61.74491.68520.19043.1884-0.15163.6195-0.0358-0.0887-0.0707-0.23460.58840.38760.5706-0.4294-0.34070.3265-0.008-0.00420.49310.06050.576785.89290.7052123.2646
71.8719-0.03160.34881.40370.56590.7554-0.2765-0.5892-0.1432-0.5020.3205-0.29960.2650.4593-0.0287-0.01780.1432-0.07420.7206-0.02140.497394.89898.0712121.4169
83.0760.0063.78232.1179-2.15229.91140.0174-0.5235-0.11550.31210.0320.17690.1248-0.1082-0.18890.3296-0.0959-0.05980.4038-0.03750.323585.74497.1159125.7641
91.788-1.97241.373.0432-2.65362.7398-0.179-0.4995-0.16480.26260.1917-0.01180.2025-0.0753-0.10080.34530.0423-0.07870.4984-0.00270.307986.05819.7344128.4179
100.04220.00910.5487-0.02940.01278.14340.2656-0.030.1422-0.03380.21310.7588-0.2468-0.0731-0.03080.43550.13-0.09230.0692-0.50320.098284.837614.7259104.0893
113.86670.9272-1.29814.324-0.04258.47540.3131-0.8897-0.2773-0.33590.17330.2820.11590.0936-0.13010.1243-0.0150.08080.5350.01240.4465106.806425.0518185.8214
123.6131-1.2899-2.34682.13922.35212.8821-0.04820.03380.4115-0.174-0.24440.0371-0.1017-0.12790.10540.4327-0.04730.31461.0149-0.19240.525299.220633.2447201.1031
134.86232.2343-0.55333.7041-1.6791.68040.1974-0.3430.50950.30850.2197-0.101-0.41320.1139-0.31150.15830.02770.01120.359-0.08780.447110.318436.4114188.6672
143.07261.16033.50852.0009-2.20934.49890.24880.53640.1053-1.7561-0.1412-1.69330.23491.4468-0.21020.4511-0.16810.03680.5434-0.07920.5572118.736538.7668184.5077
150.5535-1.0306-0.42921.85630.69260.23150.3498-0.36660.331-0.10770.26460.4149-0.6035-0.5402-0.24330.21740.1023-0.06370.55160.04890.6199101.553436.1532190.9108
160.89741.2542-0.41322.0399-0.25234.1944-0.0521-0.2727-0.115-0.31170.01740.1769-0.1832-0.16260.10010.26580.01450.05960.32780.07040.327109.822931.8408183.8213
170.6464-0.1141-0.61110.00960.05130.48510.0619-0.05250.3402-0.205-0.11310.1635-0.1126-0.1827-0.08650.7119-0.05390.38520.68670.02780.9829105.772940.891199.7599
180.92190.4272-0.11470.7518-0.16230.02950.28450.26830.469-0.0013-0.02510.7996-0.10260.3406-0.05530.42750.0456-0.26640.25050.11520.4433114.595525.0614173.0185
191.80850.78350.88841.8137-0.44861.04370.05730.31650.0373-0.1502-0.02350.1876-0.6548-0.00390.00220.73520.04240.11870.33640.03430.400691.418126.140899.299
201.90250.10081.17172.442-0.28170.7334-0.0926-0.03280.16680.49860.1135-0.1597-0.38320.0946-0.00320.84510.01610.03720.2928-0.05380.321989.973126.5938103.8486
210.2215-0.4351.42690.8925-2.67249.22880.47780.86880.0824-0.5371-0.8107-0.1046-0.180.14580.15511.02560.4129-0.26-0.58040.20090.550385.323821.8949110.6055
220.06880.1689-0.05370.3724-0.02571.28820.03550.59230.2947-0.3743-0.2637-0.2397-0.11070.42440.12570.61820.01080.14830.51850.14720.568785.801627.3046166.2133
234.39490.86870.49112.8576-0.14870.03910.29530.15330.8312-1.0213-0.4296-0.3226-0.6503-0.6212-0.11580.37760.22020.07080.05980.12150.533279.668426.4692171.1819
241.98850.5635-0.72481.6449-0.04892.84320.18270.2278-0.1488-0.3296-0.2125-0.18540.6337-0.3163-0.03510.30690.1074-0.05690.3417-0.08610.606111.624217.6281120.7828
250.00170.0121-0.0054-0.02830.0183-0.0048-0.139-0.531-0.21751.1130.25530.28730.39320.21560.0607-1.4252-0.1757-0.01170.8561-0.37210.8285105.334319.6971138.0169
263.9918-0.6897-0.83272.76450.2893.46590.2449-0.49160.10140.19020.10330.0228-0.68910.1391-0.29680.33870.067-0.00140.2969-0.08690.5385114.821327.3453128.7913
270.481-0.6418-0.45680.67430.69282.59480.1122-0.115-0.28120.0205-0.01410.2098-0.19-0.5675-0.1810.22010.1133-0.0160.5183-0.00270.4103109.125622.9461122.8821
286.5961.3532-1.29986.2342-2.10567.9371-0.0043-0.48610.36190.4611-0.1738-0.3887-0.208-0.05990.01430.2744-0.1690.05590.2557-0.04830.4549118.055322.3511127.1533
292.5007-0.7292-1.24062.25181.21663.9895-0.3743-0.63770.00660.091-0.18780.6493-0.14970.15050.26050.32640.0310.06360.375-0.00220.4107118.575819.1863122.7905
302.44312.45382.76746.01634.41293.8418-0.0719-0.22350.32160.2129-0.3693-0.17760.411-0.04430.34570.304-0.1116-0.0070.32360.06940.423386.492923.0487183.0153
311.59650.559-0.70463.59790.34713.04060.31250.01480.41880.10110.13980.12220.38710.1029-0.24220.1817-0.0604-0.00080.38540.08960.466885.308516.8551193.0317
320.7047-0.32780.29350.74920.07532.4299-0.0178-0.2356-0.04820.0786-0.0837-0.20970.21470.17230.08170.27580.00260.02530.34920.04890.466584.681117.1833186.0109
330.51910.05040.24951.0453-0.3671.3140.0660.2272-0.044-0.3073-0.29360.7316-0.1103-0.15940.24650.51410.1289-0.12350.4046-0.01730.4998104.787317.7207161.8585
344.81751.03233.84120.25330.84343.0381-0.1579-0.386-0.0526-0.01660.2139-0.03670.2575-0.43470.14560.84460.00640.00470.41770.02510.6859110.22139.3269162.1883
351.2713-2.9761-0.56442.0096-3.47644.16070.7283-0.1172-1.3899-0.72950.21740.54840.6064-0.5551-0.79150.7822-0.0785-0.06630.6566-0.12320.6866111.09876.4383164.2017
362.5386-1.04060.42342.3949-4.43149.27560.27080.2183-0.7173-0.44080.40380.61050.5239-0.2684-0.57450.2975-0.1897-0.22920.76570.19190.691897.201114.8478157.7905
371.26691.03830.94881.391.2361.23870.14960.298-0.18350.10680.0722-0.11170.58540.1258-0.16180.46950.06520.01710.25440.03970.3181111.212114.4712167.9792
382.7031-0.12142.3556-0.0274-0.22522.09330.27190.1421-0.18530.29670.041-0.25160.0578-0.2863-0.10070.75340.2329-0.16420.515-0.13150.4858110.881712.8436100.1764
390.30230.25141.2010.1889-1.17511.98550.34270.8873-0.5313-0.1923-0.99311.0145-0.14960.32080.06260.75720.3244-0.11390.4864-0.24770.5237119.366713.8649104.4015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 17 )
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 22 )
4X-RAY DIFFRACTION4chain 'A' and (resid 23 through 29 )
5X-RAY DIFFRACTION5chain 'A' and (resid 30 through 37 )
6X-RAY DIFFRACTION6chain 'A' and (resid 38 through 47 )
7X-RAY DIFFRACTION7chain 'A' and (resid 48 through 64 )
8X-RAY DIFFRACTION8chain 'A' and (resid 65 through 73 )
9X-RAY DIFFRACTION9chain 'A' and (resid 74 through 91 )
10X-RAY DIFFRACTION10chain 'A' and (resid 92 through 98 )
11X-RAY DIFFRACTION11chain 'B' and (resid 4 through 22 )
12X-RAY DIFFRACTION12chain 'B' and (resid 23 through 29 )
13X-RAY DIFFRACTION13chain 'B' and (resid 30 through 37 )
14X-RAY DIFFRACTION14chain 'B' and (resid 38 through 42 )
15X-RAY DIFFRACTION15chain 'B' and (resid 43 through 53 )
16X-RAY DIFFRACTION16chain 'B' and (resid 54 through 73 )
17X-RAY DIFFRACTION17chain 'B' and (resid 74 through 87 )
18X-RAY DIFFRACTION18chain 'B' and (resid 88 through 99 )
19X-RAY DIFFRACTION19chain 'C' and (resid 6 through 47 )
20X-RAY DIFFRACTION20chain 'C' and (resid 48 through 72 )
21X-RAY DIFFRACTION21chain 'C' and (resid 73 through 98 )
22X-RAY DIFFRACTION22chain 'D' and (resid 8 through 64 )
23X-RAY DIFFRACTION23chain 'D' and (resid 65 through 99 )
24X-RAY DIFFRACTION24chain 'E' and (resid 7 through 21 )
25X-RAY DIFFRACTION25chain 'E' and (resid 22 through 29 )
26X-RAY DIFFRACTION26chain 'E' and (resid 30 through 48 )
27X-RAY DIFFRACTION27chain 'E' and (resid 49 through 64 )
28X-RAY DIFFRACTION28chain 'E' and (resid 65 through 72 )
29X-RAY DIFFRACTION29chain 'E' and (resid 73 through 94 )
30X-RAY DIFFRACTION30chain 'F' and (resid 7 through 17 )
31X-RAY DIFFRACTION31chain 'F' and (resid 18 through 42 )
32X-RAY DIFFRACTION32chain 'F' and (resid 43 through 97 )
33X-RAY DIFFRACTION33chain 'G' and (resid 7 through 29 )
34X-RAY DIFFRACTION34chain 'G' and (resid 30 through 37 )
35X-RAY DIFFRACTION35chain 'G' and (resid 38 through 47 )
36X-RAY DIFFRACTION36chain 'G' and (resid 48 through 54 )
37X-RAY DIFFRACTION37chain 'G' and (resid 55 through 98 )
38X-RAY DIFFRACTION38chain 'H' and (resid 7 through 64 )
39X-RAY DIFFRACTION39chain 'H' and (resid 65 through 99 )

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  • 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

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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

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