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- PDB-5cwf: Crystal structure of de novo designed helical repeat protein DHR8 -

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Basic information

Entry
Database: PDB / ID: 5cwf
TitleCrystal structure of de novo designed helical repeat protein DHR8
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBhabha, G. / Ekiert, D.C.
CitationJournal: Nature / Year: 2015
Title: Exploring the repeat protein universe through computational protein design.
Authors: Brunette, T.J. / Parmeggiani, F. / Huang, P.S. / Bhabha, G. / Ekiert, D.C. / Tsutakawa, S.E. / Hura, G.L. / Tainer, J.A. / Baker, D.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 6, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: 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 / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed helical repeat protein
B: Designed helical repeat protein
C: Designed helical repeat protein
D: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,78336
Polymers85,5004
Non-polymers1,28232
Water6,575365
1
A: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6969
Polymers21,3751
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,81612
Polymers21,3751
Non-polymers44111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6969
Polymers21,3751
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5756
Polymers21,3751
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.690, 76.360, 133.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETASPASPchain AAA1 - 1771 - 177
2ASPASPASNASNchain BBB3 - 1803 - 180
3ASPASPGLUGLUchain CCC3 - 1793 - 179
4METMETALAALAchain DDD1 - 1761 - 176

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Components

#1: Protein
Designed helical repeat protein


Mass: 21375.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.19 M Calcium chloride, 0.095 M HEPES, pH 7.5, 26.6% (v/v) PEG 400, 5% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.111 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.111 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 72203 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 30.44 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.096 / Χ2: 0.99 / Net I/σ(I): 12.11 / Num. measured all: 512567
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.857.20.4781.8481.0738070526252601.992100
1.85-1.90.6441.4051.4637240513951351.51499.9
1.9-1.950.7391.0631.9636201498949871.145100
1.95-2.010.8410.762.7435581489248920.818100
2.01-2.080.8970.5413.8934233470747070.583100
2.08-2.150.9320.4115.0233283456245620.442100
2.15-2.230.9630.3016.8332252443644350.325100
2.23-2.320.9730.248.4430768425142470.25999.9
2.32-2.430.9820.18810.4629469407340720.202100
2.43-2.550.9880.15412.4628168392339220.166100
2.55-2.680.9890.13813.826660372437220.14899.9
2.68-2.850.9910.11715.9825080354335430.126100
2.85-3.040.9960.08719.6823253333233320.094100
3.04-3.290.9960.07123.8521162310831080.077100
3.29-3.60.9970.05927.919121288328800.06499.9
3.6-4.020.9970.05131.0816649261426110.05699.9
4.02-4.650.9980.04434.5515518231523140.047100
4.65-5.690.9990.04332.9413581199319920.04799.9
5.69-8.050.9990.03533.4910612157315720.03899.9
8.050.9990.02734.8556669389100.0397

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.38 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 3591 4.98 %RANDOM
Rwork0.1935 68561 --
obs0.1949 72152 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 229.64 Å2 / Biso mean: 47.0989 Å2 / Biso min: 16.56 Å2
Refinement stepCycle: final / Resolution: 1.8→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5338 0 32 366 5736
Biso mean--36.62 41.3 -
Num. residues----704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085537
X-RAY DIFFRACTIONf_angle_d1.0187444
X-RAY DIFFRACTIONf_chiral_restr0.041877
X-RAY DIFFRACTIONf_plane_restr0.0051018
X-RAY DIFFRACTIONf_dihedral_angle_d12.6792206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3897X-RAY DIFFRACTION6.832TORSIONAL
12B3897X-RAY DIFFRACTION6.832TORSIONAL
13C3897X-RAY DIFFRACTION6.832TORSIONAL
14D3897X-RAY DIFFRACTION6.832TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82380.35781290.313826052734100
1.8238-1.84880.32241450.29626052750100
1.8488-1.87520.25681350.278325782713100
1.8752-1.90320.31411260.267626212747100
1.9032-1.93290.27391440.256425732717100
1.9329-1.96460.2621390.249726392778100
1.9646-1.99850.29941360.22225912727100
1.9985-2.03480.24391370.220426142751100
2.0348-2.07390.26281360.206526152751100
2.0739-2.11630.22671410.198326132754100
2.1163-2.16230.19811410.186126202761100
2.1623-2.21260.21431330.184826022735100
2.2126-2.26790.22781350.188626012736100
2.2679-2.32920.23761400.189526402780100
2.3292-2.39780.231380.180926312769100
2.3978-2.47520.2091440.178826262770100
2.4752-2.56360.21891350.173726372772100
2.5636-2.66620.23241360.182426152751100
2.6662-2.78760.21141410.191926452786100
2.7876-2.93450.22431370.193926462783100
2.9345-3.11830.23581380.181326532791100
3.1183-3.3590.21991420.185826632805100
3.359-3.69690.21281350.171926732808100
3.6969-4.23150.18191420.165226962838100
4.2315-5.32980.19891380.178127212859100
5.3298-44.39350.21741480.22922838298699
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)
11.41271.1156-0.73881.1496-0.06971.58570.23990.06820.6640.2693-0.0907-0.088-0.4223-0.11530.85830.3134-0.01020.03110.1369-0.05940.50212.630254.1861111.0971
20.8014-0.2033-0.35940.364-0.16140.33250.1994-0.20330.08510.10940.0454-0.08010.1597-0.14710.00380.19370.01390.00460.2627-0.05690.30369.844746.3356118.2035
30.4246-0.2717-0.07080.5175-0.16230.1369-0.1150.1530.65160.11540.08940.1671-0.23610.5781-0.07910.2651-0.05710.01410.3523-0.07160.328622.887749.1096116.4698
41.4956-0.6589-0.26680.3958-0.14980.67830.1257-0.05810.36670.067-0.16320.0574-0.0340.2186-0.00570.2303-0.04380.0040.3618-0.06430.305421.356540.5242117.7416
50.4241-0.49510.23091.1370.36770.9186-0.0040.1123-0.14160.17110.08310.14650.3025-0.50450.00440.1842-0.0179-0.01160.4549-0.0150.25821.346632.725114.0658
60.7268-0.01950.30530.8327-0.02360.19850.1153-0.363-0.02010.348-0.1908-0.1571-0.16511.0065-0.00010.2849-0.0638-0.00550.5587-0.06440.325332.070834.23121.9722
70.2674-0.06250.29020.59930.23540.772-0.22720.1988-0.6409-0.0874-0.1069-0.64680.86240.2481-0.09390.3834-0.0252-0.00360.4658-0.08840.447827.80325.7331115.9661
80.0812-0.08960.01870.0894-0.04220.010.02530.0374-0.0034-0.03780.06970.0640.0360.11370.35170.94890.6523-0.4610.3093-0.03260.587220.5844-0.5671110.7216
90.6973-0.36460.30360.73350.28040.82620.1404-0.1888-0.4073-0.2933-0.0911-0.21830.73130.4530.77930.45390.1386-0.01750.3570.09680.338418.64675.4139118.4965
100.3672-0.1232-0.3050.2640.12070.27110.1244-0.074-0.0753-0.1964-0.004-0.2080.16940.7306-0.00880.38950.09010.03680.41880.02710.343319.467114.133114.822
110.9629-0.33990.33710.1433-0.04760.3936-0.0028-0.4964-0.411-0.13090.14120.16410.101-0.28830.04090.30.0202-0.03410.27470.09540.31848.057912.0378121.4674
120.1662-0.11930.01011.0021-0.53960.302-0.09770.02830.17520.0188-0.1142-0.1127-0.07270.6299-00.33080.0146-0.03350.3250.01180.299313.641420.993114.5685
130.2111-0.15490.15840.6040.37830.5668-0.1883-0.391-0.06820.3555-0.06010.44150.2002-0.3937-0.18150.31430.02830.01180.30290.07040.3444.585120.2074124.4235
140.8222-0.2562-0.3320.29420.00580.30590.016-0.0686-0.17030.10780.05190.0694-0.15590.28210.00560.28140.0356-0.06670.2613-0.01680.25528.468129.0451120.5916
150.9854-0.7461-1.0590.56020.82921.69960.1024-1.3050.63280.15760.3822-0.14330.0609-0.26530.18460.45650.1243-0.14571.0199-0.09940.683539.760219.325989.0426
161.8890.31241.30281.66770.42930.9237-0.4690.3396-0.4543-0.5203-0.1494-0.24850.51970.6554-1.03710.39290.21050.1410.41550.00830.434333.025715.205781.9107
170.43830.07580.60251.9287-0.05780.89660.0549-0.42150.5438-0.39690.1383-0.42430.22321.05980.04740.3010.12730.07580.4758-0.01320.484734.951127.38181.0713
180.8827-0.5198-0.33110.47530.06360.2332-0.1673-0.0694-0.3112-0.1891-0.1736-0.30150.62530.1821-0.03220.36430.05330.05130.35420.03080.307225.50219.874686.3026
190.8404-0.2106-0.10110.09030.10541.16920.03270.11430.3319-0.4154-0.1706-0.7119-0.37140.4648-0.69380.3580.03650.1370.29630.06050.366227.030731.289378.2275
200.6224-0.32640.06620.24310.08240.4427-0.1565-0.133-0.07150.1241-0.21040.28250.4783-0.2591-0.00890.2540.0379-0.00030.2611-0.01940.227917.870425.134484.9848
210.4864-0.19610.26350.6248-0.28080.3330.0650.26760.4463-0.35-0.4957-0.065-0.1729-0.0433-0.13560.34430.07970.06540.29410.02510.376318.655934.354475.0779
220.6030.01160.01290.5986-0.51090.4550.23190.38390.0524-0.24860.2728-0.23640.1450.0280.23830.28510.0108-0.02290.3512-0.09140.258510.054330.066379.5543
230.71350.1987-0.32790.3886-0.11640.4592-0.17020.14760.31790.1354-0.23731.1335-0.0241-0.2452-0.00960.2398-0.0044-0.00550.2468-0.04210.4503-15.170624.570788.1028
240.2577-0.3167-0.12230.706-0.0960.2027-0.04170.16570.1406-0.01110.15360.2282-0.0640.1087-0.00010.2282-0.025-0.05060.23190.01140.28-7.044427.913481.858
250.53330.2628-0.39720.3689-0.28870.33420.0555-0.06920.0150.1687-0.07310.42230.4756-0.1149-0.02630.3725-0.0334-0.07340.2117-0.04140.2684-9.16315.188683.656
260.3298-0.4879-0.01992.378-0.0040.3243-0.07340.04290.0529-0.02590.07860.2126-0.02310.0361-0.00010.2927-0.0036-0.02920.211-0.02480.23561.728116.241282.736
270.5812-0.0282-0.01930.2650.31760.4867-0.14070.2796-0.336-0.44440.1423-0.0820.79410.08240.04560.507-0.0295-0.00110.1997-0.05090.24476.35586.007477.7618
280.30210.28610.04340.29840.20040.6536-0.1678-0.0388-0.54120.21040.1347-0.41760.44410.63370.03890.45740.0107-0.04760.42770.00810.368814.210510.964884.6469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:21 )A1 - 21
2X-RAY DIFFRACTION2( CHAIN A AND RESID 22:44 )A22 - 44
3X-RAY DIFFRACTION3( CHAIN A AND RESID 45:67 )A45 - 67
4X-RAY DIFFRACTION4( CHAIN A AND RESID 68:111 )A68 - 111
5X-RAY DIFFRACTION5( CHAIN A AND RESID 112:134 )A112 - 134
6X-RAY DIFFRACTION6( CHAIN A AND RESID 135:156 )A135 - 156
7X-RAY DIFFRACTION7( CHAIN A AND RESID 157:177 )A157 - 177
8X-RAY DIFFRACTION8( CHAIN B AND RESID 3:24 )B3 - 24
9X-RAY DIFFRACTION9( CHAIN B AND RESID 25:65 )B25 - 65
10X-RAY DIFFRACTION10( CHAIN B AND RESID 66:89 )B66 - 89
11X-RAY DIFFRACTION11( CHAIN B AND RESID 90:111 )B90 - 111
12X-RAY DIFFRACTION12( CHAIN B AND RESID 112:134 )B112 - 134
13X-RAY DIFFRACTION13( CHAIN B AND RESID 135:156 )B135 - 156
14X-RAY DIFFRACTION14( CHAIN B AND RESID 157:180 )B157 - 180
15X-RAY DIFFRACTION15( CHAIN C AND RESID 3:24 )C3 - 24
16X-RAY DIFFRACTION16( CHAIN C AND RESID 25:44 )C25 - 44
17X-RAY DIFFRACTION17( CHAIN C AND RESID 45:65 )C45 - 65
18X-RAY DIFFRACTION18( CHAIN C AND RESID 66:89 )C66 - 89
19X-RAY DIFFRACTION19( CHAIN C AND RESID 90:111 )C90 - 111
20X-RAY DIFFRACTION20( CHAIN C AND RESID 112:134 )C112 - 134
21X-RAY DIFFRACTION21( CHAIN C AND RESID 135:156 )C135 - 156
22X-RAY DIFFRACTION22( CHAIN C AND RESID 157:179 )C157 - 179
23X-RAY DIFFRACTION23( CHAIN D AND RESID 1:21 )D1 - 21
24X-RAY DIFFRACTION24( CHAIN D AND RESID 22:44 )D22 - 44
25X-RAY DIFFRACTION25( CHAIN D AND RESID 45:67 )D45 - 67
26X-RAY DIFFRACTION26( CHAIN D AND RESID 68:134 )D68 - 134
27X-RAY DIFFRACTION27( CHAIN D AND RESID 135:156 )D135 - 156
28X-RAY DIFFRACTION28( CHAIN D AND RESID 157:176 )D157 - 176

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