[English] 日本語
Yorodumi
- PDB-5mad: GFP-binding DARPin 3G61 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mad
TitleGFP-binding DARPin 3G61
Components
  • 3G61
  • 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
DI(HYDROXYETHYL)ETHER / Green fluorescent protein
Similarity search - Component
Biological speciessynthetic construct (others)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3G61
B: Green fluorescent protein
C: 3G61
D: Green fluorescent protein
E: 3G61
F: Green fluorescent protein
G: 3G61
H: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,75617
Polymers177,8848
Non-polymers8729
Water22,4471246
1
A: 3G61
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7895
Polymers44,4712
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: 3G61
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7895
Polymers44,4712
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: 3G61
F: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6004
Polymers44,4712
Non-polymers1292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: 3G61
H: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5773
Polymers44,4712
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.420, 83.070, 162.000
Angle α, β, γ (deg.)90.00, 94.59, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3G61


Mass: 17017.029 Da / Num. of mol.: 4
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.: 4
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: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1246 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic, pH 5.5, 30% PEG 4000, 0.2 M Ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.53→48.76 Å / Num. obs: 237243 / % possible obs: 98.8 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.79
Reflection shellResolution: 1.53→1.67 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 1.39 / CC1/2: 0.752

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→48.76 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 11863 5.01 %
Rwork0.1706 --
obs0.172 236919 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12068 0 57 1246 13371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612726
X-RAY DIFFRACTIONf_angle_d0.83817254
X-RAY DIFFRACTIONf_dihedral_angle_d15.0177512
X-RAY DIFFRACTIONf_chiral_restr0.0521909
X-RAY DIFFRACTIONf_plane_restr0.0052277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5299-1.54730.38683910.37487482X-RAY DIFFRACTION99
1.5473-1.56550.40364190.35577514X-RAY DIFFRACTION99
1.5655-1.58460.34814020.34037483X-RAY DIFFRACTION99
1.5846-1.60470.35053890.33127542X-RAY DIFFRACTION99
1.6047-1.62580.34113810.31027541X-RAY DIFFRACTION99
1.6258-1.64810.31084170.29397417X-RAY DIFFRACTION99
1.6481-1.67160.32474340.28117368X-RAY DIFFRACTION98
1.6716-1.69660.30753780.27677096X-RAY DIFFRACTION94
1.6966-1.72310.29714110.25887343X-RAY DIFFRACTION97
1.7231-1.75130.27294100.23727511X-RAY DIFFRACTION100
1.7513-1.78150.26914140.22197534X-RAY DIFFRACTION99
1.7815-1.81390.26933800.21457529X-RAY DIFFRACTION99
1.8139-1.84880.22783840.20377600X-RAY DIFFRACTION100
1.8488-1.88660.23873870.2017606X-RAY DIFFRACTION100
1.8866-1.92760.22633870.19187525X-RAY DIFFRACTION100
1.9276-1.97240.22433890.18367561X-RAY DIFFRACTION99
1.9724-2.02180.23053790.18847592X-RAY DIFFRACTION99
2.0218-2.07640.21624280.18267479X-RAY DIFFRACTION99
2.0764-2.13750.20413540.1717271X-RAY DIFFRACTION95
2.1375-2.20650.20393980.1597412X-RAY DIFFRACTION98
2.2065-2.28540.19093970.1557570X-RAY DIFFRACTION99
2.2854-2.37690.19994090.15967573X-RAY DIFFRACTION100
2.3769-2.48510.20593990.15567574X-RAY DIFFRACTION100
2.4851-2.61610.1783800.1577620X-RAY DIFFRACTION100
2.6161-2.780.20243790.16237582X-RAY DIFFRACTION99
2.78-2.99460.17683950.17267483X-RAY DIFFRACTION98
2.9946-3.29590.19933550.17097435X-RAY DIFFRACTION97
3.2959-3.77260.18163870.15137678X-RAY DIFFRACTION99
3.7726-4.75250.14984300.12377534X-RAY DIFFRACTION99
4.7525-48.78450.16274000.15237601X-RAY DIFFRACTION97
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)
10.00080.0046-0.00320.0858-0.10020.10570.08810.4306-0.0759-0.1165-0.3606-0.2218-0.05830.3706-0.00010.37530.0075-0.04710.40640.00390.311959.9320.672245.7491
20.25990.10970.09390.41170.35240.7871-0.0181-0.0427-0.1962-0.05340.06610.0318-0.0315-0.4094-00.2913-0.0091-0.03580.35380.02110.296555.1099-0.01455.207
30.28680.14010.00490.61310.18520.78480.0584-0.3122-0.14650.1157-0.0830.02910.0067-0.54240.00010.2919-0.0168-0.00770.50610.09640.295554.3374-1.992473.1137
40.04010.0192-0.01760.04110.05410.08260.118-0.0530.02520.1648-0.2880.0835-0.1948-0.48460.00010.3775-0.0255-0.03680.55340.06170.274457.72544.300685.7822
50.36930.1427-0.3710.5380.13550.5529-0.1978-0.12050.18560.33640.3588-0.3665-0.6050.30270.51710.4846-0.02040.05310.1690.04730.337987.04519.815862.1996
60.5613-0.3765-0.62920.24110.39840.66950.03340.17920.0858-0.1177-0.0413-0.1877-0.04080.38380.00580.2858-0.00580.01870.24510.030.336190.0057-2.214758.1364
70.60360.35540.41380.2530.27460.3206-0.05480.19520.0587-0.18620.0548-0.0756-0.38860.0013-0.01720.41310.0264-0.00390.1350.05840.26373.252212.980358.3468
80.726-0.4024-0.29410.26250.3280.8283-0.1581-0.28710.0534-0.01350.2349-0.1563-0.04030.290.4610.3744-0.03130.0191-0.01390.0230.285880.73363.537268.7142
90.8057-0.0503-0.47770.3446-0.20470.4842-0.1402-0.25120.16130.12170.3683-0.2257-0.11950.49590.25430.3035-0.0674-0.00090.2225-0.02890.303589.31443.604368.356
100.57410.3523-0.26410.2518-0.06310.4058-0.23160.0589-0.3605-0.03020.12370.00540.22570.0047-0.26020.39170.07980.04240.13720.01490.382283.4716-15.567262.6932
110.1347-0.0425-0.05890.1178-0.05740.0671-0.1574-0.2524-0.1536-0.01220.14010.1884-0.03310.10790.00010.30790.0299-0.00790.20530.01330.259271.08045.750370.0275
120.1905-0.2753-0.07220.5280.05960.35-0.1499-0.1149-0.29940.05950.12380.30120.0089-0.13540.00270.2618-0.01540.00250.1166-0.00030.330274.467-1.983366.6195
130.5250.0765-0.15690.2924-0.25460.2435-0.2038-0.2563-0.4169-0.02590.2342-0.30740.0308-0.0322-0.10560.2737-0.04620.06430.04910.02710.382977.6137-9.174965.208
140.3104-0.03640.00590.2192-0.32160.47090.01110.05610.0957-0.12440.1292-0.18-0.2324-0.02450.02180.34710.00110.00760.1783-0.00060.323974.91177.652662.3104
150.0287-0.0419-0.00580.0947-0.01570.01130.06620.63420.0812-0.3196-0.2163-0.44460.20330.4782-0.00010.35310.05320.10690.4321-0.00360.388695.9614-7.945450.2668
160.16990.24660.06690.34440.05690.17370.05820.1848-0.0556-0.3238-0.01040.1034-0.2808-0.0505-00.43480.04820.01920.26340.02260.306671.83456.675754.8877
17-0.00030.01810.0170.09210.09260.0809-0.0146-0.65830.32630.2437-0.3140.0929-0.0107-0.2512-0.00010.36470.0682-0.04120.4236-0.09250.283482.62141.6301122.7064
180.0171-0.0227-0.02970.03310.09780.6766-0.0806-0.27970.04820.0890.10040.0204-0.08030.0751-0.00020.32260.0349-0.03560.2361-0.0030.260186.77411.4457117.92
190.4643-0.3123-0.32620.3335-0.06090.6940.01120.1167-0.0394-0.079-0.0334-0.07910.09870.34730.00220.28740.0291-0.01630.2210.01650.261988.3849-0.4385103.3394
200.0252-0.0164-0.00780.0185-0.01050.0146-0.05520.4274-0.0480.2157-0.02880.0932-0.37610.5431-0.00020.3348-0.04270.00350.3620.0390.233793.41935.021492.3667
210.05320.0910.04760.1390.05810.10650.285-0.00430.321-0.1948-0.206-0.01710.5314-0.0475-00.40170.04480.00450.2893-0.03740.288584.6417-6.112688.8837
220.0422-0.05030.02830.0569-0.04210.13710.06920.04730.0466-0.1342-0.2747-0.37280.02010.2170.00010.3590.0384-0.02350.32030.05420.316185.39493.978982.3726
230.5193-0.0936-0.37170.7154-0.32080.4568-0.07670.37150.60620.05640.27770.4481-0.3444-0.19910.13510.39680.06390.08880.31410.0880.523456.036810.646107.2696
240.65670.3393-0.75160.3025-0.40510.79160.0030.01980.2140.18060.12460.373-0.074-0.35720.01650.28210.04750.04310.28610.07360.380252.5798-1.2865110.2143
250.3682-0.0605-0.30050.2115-0.12290.38410.2484-0.02950.48420.36120.00040.2895-0.1663-0.03110.24210.37290.06950.08640.17740.05890.420566.368514.7803107.21
261.50310.472-0.57911.4687-0.5910.7072-0.26610.81810.2763-0.1360.5320.35830.1083-0.60420.35080.24920.0516-0.010.26960.19220.322956.29951.433599.245
270.3801-0.4437-0.06070.5647-0.01710.2509-0.2432-0.008-0.39830.17950.1681-0.0550.1799-0.0894-0.10870.3124-0.0740.08350.18840.01470.346358.997-14.8498105.929
280.14340.00040.00180.19130.14330.098-0.05240.29310.1130.06950.0826-0.0407-0.0906-0.244600.27370.0254-0.00780.22690.07040.266871.53356.282598.396
291.00630.0878-0.48260.05780.0330.2968-0.22810.2992-0.308-0.03080.27070.10010.1583-0.03280.05750.29850.0430.03580.13630.06680.305466.5023-4.435101.9111
300.25430.1509-0.03950.27060.14620.10490.01970.13550.29380.1920.19190.265-0.0763-0.1540.05560.31050.05070.02790.20540.10070.352167.70068.8977105.3745
310.3779-0.1081-0.11810.06880.08090.1141-0.0299-0.84950.17420.4245-0.03090.71110.4453-0.0094-0.00130.39830.01550.18290.41170.07260.501146.5836-6.9177118.1854
320.2219-0.19710.03560.2933-0.06940.0904-0.0471-0.30060.34330.34990.10530.0799-0.1114-0.0658-0.00280.37760.01510.03030.2011-0.00550.331770.74767.4451113.4096
330.0453-0.01230.05520.2703-0.3820.5687-0.03611.003-0.0895-0.0799-0.00760.2881-0.2846-0.4656-0.00920.38040.0595-0.03430.93050.04930.377269.529712.5571129.6335
340.7392-0.2718-0.11510.25720.15590.96020.06860.0269-0.07710.0715-0.0314-0.00590.1319-0.42220.0040.245-0.00520.00910.5324-0.03820.276972.559911.5005148.0854
350.1661-0.17450.00040.1541-0.030.27430.0143-0.12440.04230.03250.0619-0.02810.0406-0.0262-00.3159-0.00720.0080.5267-0.01820.319181.105811.6787165.3791
360.0014-0.00240.01350.0474-0.00580.0257-0.28430.02040.28380.2089-0.05950.0885-0.0211-0.2086-0.00030.47990.0669-0.00380.6659-0.0580.342974.983618.5918170.9982
370.0092-0.01080.01290.0125-0.01280.01270.07320.04260.25160.0011-0.15280.19390.15870.1171-0.00010.53-0.08360.21590.58340.08960.719197.716529.8694132.2576
380.57360.5534-0.15730.60760.09971.41180.2657-0.33830.29580.20590.37840.0056-0.04171.03480.74650.29250.0336-0.00160.7398-0.14750.3185110.636812.5036141.4991
390.02210.00810.02040.63470.49450.41520.10040.2704-0.00960.08370.4544-0.0246-0.15060.79440.49330.23890.07610.00230.752-0.07150.3581109.687811.2591137.0088
400.30820.1140.24710.04680.10310.2170.3383-0.0034-0.087-0.20850.18590.0104-0.29990.46440.19580.28890.01570.04970.5971-0.0390.3225101.460914.301130.5718
410.0623-0.01750.00020.00350.00250.0001-0.11860.22610.25680.14020.3306-0.31820.1680.57060.03770.30430.1805-0.06210.7497-0.19060.3871112.5081.3178140.0815
420.00480.0179-0.00240.0412-0.00550.0012-0.0411-0.20320.11880.10270.2056-0.21060.14440.45470.00020.2520.0612-0.03170.5121-0.10840.2914103.12116.557140.3744
430.0548-0.0525-0.09130.07580.12610.18710.24880.33140.5094-0.24180.0661-0.123-0.35710.123500.3924-0.01860.10810.3416-0.01690.486992.770625.8849139.4481
441.15650.0448-1.03470.8794-0.0761.3088-0.0216-0.72960.35370.01850.4022-0.19840.14110.93180.56950.2772-0.0207-0.02130.5874-0.17840.336104.684714.0228146.9711
450.32060.2908-0.16070.2687-0.14340.0738-0.2786-0.0756-0.25750.14680.1455-0.13940.23770.25150.00080.41890.2041-0.00510.4033-0.02230.3558101.2134-3.0474143.5279
460.0814-0.17030.12650.5503-0.52380.53550.0777-0.35230.1351-0.05840.0714-0.07130.05480.17810.10870.1963-0.0150.0380.4453-0.15210.331489.711418.7985150.4386
470.4377-0.0620.25430.116-0.19620.42250.0989-0.55210.01270.13550.00280.28580.18980.17210.17010.280.00860.02510.4125-0.08520.284792.396310.8501147.4642
480.50010.2075-0.52910.7108-0.24920.3872-0.0476-0.46550.0565-0.01320.20360.00860.00140.19030.29880.30830.00540.00690.3377-0.10610.263994.940914.1789147.9034
490.16470.23130.14370.584-0.10030.38930.06790.34260.1029-0.03330.0125-0.0405-0.0470.23230.05740.25680.0494-0.00160.514-0.08080.265597.24310.0842133.2179
500.12490.11780.05180.08880.03420.05450.1579-0.4919-0.27060.2424-0.15330.01410.3291-0.23430.00010.3934-0.0171-0.01810.5912-0.01350.3453117.70788.0774200.9356
510.05230.03970.01330.04220.01180.003-0.0936-0.2951-0.12350.08860.0758-0.1745-0.54120.37960.00010.3788-0.0095-0.05280.5041-0.08670.3965124.33215.6909199.2028
520.03720.0110.06470.2271-0.01250.0795-0.0879-0.4762-0.0930.05030.0761-0.05720.0150.063400.29730.0325-0.00460.35680.01070.312116.46845.2386194.4649
530.09240.08270.00730.0873-0.04630.0875-0.0071-0.26530.16160.1088-0.11570.0055-0.05110.364-00.2508-0.0132-0.01770.3636-0.02570.2887121.22914.4869188.9595
540.26310.0103-0.05470.202-0.08830.2030.02380.1688-0.0026-0.0905-0.01670.09890.05740.295200.26740.0281-0.0130.3061-0.03060.2727115.37829.1291182.7072
550.02490.0301-0.03570.0362-0.04460.0437-0.07810.5278-0.02840.2169-0.03560.00510.03460.54950.00010.2439-0.0024-0.01420.46570.00390.2925124.530615.8357179.4854
560.1046-0.0961-0.0820.2209-0.02910.2753-0.01440.4686-0.05870.10670.06310.02320.1686-0.034500.3020.0038-0.00680.5008-0.04550.3021113.69899.045173.9955
570.08360.09540.07960.1140.09230.0821-0.02860.5950.0850.10260.38610.0133-0.08440.58470.00780.2643-0.03680.01640.69220.02010.2708120.841318.0137169.2889
580.07280.0327-0.01410.0415-0.04210.0434-0.04530.4157-0.0565-0.04320.02080.13180.1441-0.12830.00340.3127-0.0155-0.01840.7594-0.07960.3327111.08487.6101166.0991
590.0251-0.03010.01430.0332-0.01890.02410.08880.48450.06350.14020.07620.4346-0.2079-0.266400.35440.03290.00860.79850.02220.3203107.10517.1348162.2373
600.0683-0.01250.03920.148-0.06080.1062-0.00430.35140.2554-0.0895-0.1854-0.32130.230.2413-0.04010.4318-0.02480.0160.92650.15310.3557115.128119.2176159.1443
610.02630.0420.03160.06590.04850.03030.2009-0.49140.4530.118-0.1573-0.1285-0.22720.05560.00020.4261-0.0119-0.01670.292-0.12320.405393.241429.8821197.4465
620.24410.1107-0.24060.1682-0.12870.2135-0.09870.08090.1369-0.07320.16840.1990.0172-0.2536-00.241-0.0362-0.01540.3559-0.03380.297779.859211.4618188.2722
630.1877-0.0758-0.090.405-0.31170.3268-0.0682-0.23670.1114-0.1120.09390.0511-0.1651-0.3268-00.2295-0.0363-0.01350.398-0.02390.285181.179610.9205193.8424
640.1852-0.1471-0.17340.09930.13980.14960.0408-0.4218-0.02080.09550.04630.02140.0297-0.137700.2680.0252-0.01610.421-0.04680.279689.47113.7412199.7416
650.011-0.01050.00530.00340.00110.0224-0.0161-0.2336-0.067-0.05410.2452-0.09280.3657-0.4906-0.00010.2793-0.0863-0.01250.35140.03520.331177.6630.5888189.3957
660.01980.0288-0.00350.0366-0.00510.0288-0.09610.01870.0058-0.13670.0120.2082-0.1289-0.125800.2355-0.0122-0.00120.2170.00180.252187.13245.8805189.3668
670.0455-0.04010.02110.1631-0.12170.0925-0.1047-0.29590.4509-0.03850.03080.0166-0.07170.0480.00010.2898-0.0087-0.01450.2727-0.0790.348100.955423.5515193.1897
680.85390.3086-0.16410.4423-0.49090.6047-0.1050.16370.2362-0.11670.13550.1416-0.1398-0.2480.00230.26040.019-0.02540.2496-0.01830.288886.953616.3948184.2237
690.3789-0.2023-0.22340.13130.05090.1967-0.24340.1517-0.2668-0.09980.11020.0060.24140.0092-0.05920.3747-0.08530.04720.1926-0.04290.346988.6719-4.0074185.5244
700.13060.0522-0.01650.16360.11660.0908-0.03770.27420.097-0.3190.09650.02540.3194-0.1753-00.2277-0.0085-0.01990.26990.04510.304100.622118.7021179.8894
710.501-0.0011-0.29510.07160.03560.1679-0.05130.25530.0189-0.0503-0.0591-0.1251-0.0572-0.064600.26910.00150.00010.22070.00470.308497.903410.5826182.5512
721.23360.641-0.47930.2921-0.26680.3821-0.07330.05670.0914-0.08880.0494-0.0579-0.04870.018300.26190.013-0.00590.1768-0.00750.243796.662312.9798185.4546
730.4243-0.38220.22880.47880.08810.55740.0576-0.36170.0430.0795-0.06-0.0046-0.0221-0.1696-00.2703-0.01920.00160.3395-0.00620.231190.12838.7384198.0788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 147 )
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 165 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 64 )
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 81 )
8X-RAY DIFFRACTION8chain 'B' and (resid 82 through 104 )
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 128 )
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 147 )
11X-RAY DIFFRACTION11chain 'B' and (resid 148 through 158 )
12X-RAY DIFFRACTION12chain 'B' and (resid 159 through 170 )
13X-RAY DIFFRACTION13chain 'B' and (resid 171 through 187 )
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 208 )
15X-RAY DIFFRACTION15chain 'B' and (resid 209 through 218 )
16X-RAY DIFFRACTION16chain 'B' and (resid 219 through 233 )
17X-RAY DIFFRACTION17chain 'C' and (resid 12 through 24 )
18X-RAY DIFFRACTION18chain 'C' and (resid 25 through 58 )
19X-RAY DIFFRACTION19chain 'C' and (resid 59 through 124 )
20X-RAY DIFFRACTION20chain 'C' and (resid 125 through 133 )
21X-RAY DIFFRACTION21chain 'C' and (resid 134 through 147 )
22X-RAY DIFFRACTION22chain 'C' and (resid 148 through 166 )
23X-RAY DIFFRACTION23chain 'D' and (resid 0 through 24 )
24X-RAY DIFFRACTION24chain 'D' and (resid 25 through 64 )
25X-RAY DIFFRACTION25chain 'D' and (resid 68 through 91 )
26X-RAY DIFFRACTION26chain 'D' and (resid 92 through 128 )
27X-RAY DIFFRACTION27chain 'D' and (resid 129 through 147 )
28X-RAY DIFFRACTION28chain 'D' and (resid 148 through 158 )
29X-RAY DIFFRACTION29chain 'D' and (resid 159 through 187 )
30X-RAY DIFFRACTION30chain 'D' and (resid 188 through 208 )
31X-RAY DIFFRACTION31chain 'D' and (resid 209 through 218 )
32X-RAY DIFFRACTION32chain 'D' and (resid 219 through 233 )
33X-RAY DIFFRACTION33chain 'E' and (resid 9 through 35 )
34X-RAY DIFFRACTION34chain 'E' and (resid 36 through 133 )
35X-RAY DIFFRACTION35chain 'E' and (resid 134 through 157 )
36X-RAY DIFFRACTION36chain 'E' and (resid 158 through 168 )
37X-RAY DIFFRACTION37chain 'F' and (resid 4 through 11 )
38X-RAY DIFFRACTION38chain 'F' and (resid 12 through 24 )
39X-RAY DIFFRACTION39chain 'F' and (resid 25 through 36 )
40X-RAY DIFFRACTION40chain 'F' and (resid 37 through 48 )
41X-RAY DIFFRACTION41chain 'F' and (resid 49 through 56 )
42X-RAY DIFFRACTION42chain 'F' and (resid 57 through 64 )
43X-RAY DIFFRACTION43chain 'F' and (resid 68 through 91 )
44X-RAY DIFFRACTION44chain 'F' and (resid 92 through 128 )
45X-RAY DIFFRACTION45chain 'F' and (resid 129 through 147 )
46X-RAY DIFFRACTION46chain 'F' and (resid 148 through 158 )
47X-RAY DIFFRACTION47chain 'F' and (resid 159 through 170 )
48X-RAY DIFFRACTION48chain 'F' and (resid 171 through 198 )
49X-RAY DIFFRACTION49chain 'F' and (resid 199 through 231 )
50X-RAY DIFFRACTION50chain 'G' and (resid 9 through 23 )
51X-RAY DIFFRACTION51chain 'G' and (resid 24 through 35 )
52X-RAY DIFFRACTION52chain 'G' and (resid 36 through 49 )
53X-RAY DIFFRACTION53chain 'G' and (resid 50 through 67 )
54X-RAY DIFFRACTION54chain 'G' and (resid 68 through 91 )
55X-RAY DIFFRACTION55chain 'G' and (resid 92 through 100 )
56X-RAY DIFFRACTION56chain 'G' and (resid 101 through 124 )
57X-RAY DIFFRACTION57chain 'G' and (resid 125 through 133 )
58X-RAY DIFFRACTION58chain 'G' and (resid 134 through 147 )
59X-RAY DIFFRACTION59chain 'G' and (resid 148 through 157 )
60X-RAY DIFFRACTION60chain 'G' and (resid 158 through 168 )
61X-RAY DIFFRACTION61chain 'H' and (resid 2 through 11 )
62X-RAY DIFFRACTION62chain 'H' and (resid 12 through 24 )
63X-RAY DIFFRACTION63chain 'H' and (resid 25 through 36 )
64X-RAY DIFFRACTION64chain 'H' and (resid 37 through 48 )
65X-RAY DIFFRACTION65chain 'H' and (resid 49 through 56 )
66X-RAY DIFFRACTION66chain 'H' and (resid 57 through 64 )
67X-RAY DIFFRACTION67chain 'H' and (resid 68 through 81 )
68X-RAY DIFFRACTION68chain 'H' and (resid 82 through 128 )
69X-RAY DIFFRACTION69chain 'H' and (resid 129 through 147 )
70X-RAY DIFFRACTION70chain 'H' and (resid 148 through 158 )
71X-RAY DIFFRACTION71chain 'H' and (resid 159 through 170 )
72X-RAY DIFFRACTION72chain 'H' and (resid 171 through 208 )
73X-RAY DIFFRACTION73chain 'H' and (resid 209 through 232 )

+
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