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- PDB-3lzp: Crystal Structure Analysis of the 'as-isolated' P19 protein from ... -

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Basic information

Entry
Database: PDB / ID: 3lzp
TitleCrystal Structure Analysis of the 'as-isolated' P19 protein from Campylobacter jejuni at 1.65 A at pH 9.0
ComponentsP19 protein
KeywordsTRANSPORT PROTEIN / copper binding / iron transport / iron uptake / P19 delition
Function / homology
Function and homology information


Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Iron transporter / Uncharacterized protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDoukov, T.I. / Chan, A.C.K. / Scofield, M. / Ramin, A.B. / Tom-Yew, S.A.L. / Murphy, M.E.P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure and Function of P19, a High-Affinity Iron Transporter of the Human Pathogen Campylobacter jejuni.
Authors: Chan, A.C. / Doukov, T.I. / Scofield, M. / Tom-Yew, S.A. / Ramin, A.B. / Mackichan, J.K. / Gaynor, E.C. / Murphy, M.E.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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.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 / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P19 protein
B: P19 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6938
Polymers35,1822
Non-polymers5116
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-27 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.706, 72.533, 75.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein P19 protein


Mass: 17590.859 Da / Num. of mol.: 2 / Fragment: residues 22-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / Gene: CJJ81176_1650, Gene Cj81176_1659 / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1W1R1, UniProt: A0A0H3PA01*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 50% POLYETHYLENE GLYCOL (PEG) 250, 0.1 M CHES (2-(N-CYCLOHEXYLAMINO) ETHANE SULFONIC ACID) BUFFER PH 9.0, CRYO FROZEN WITHOUT ANY ADDITION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2006
Details: 1m Rh coated cylindrical mirror; Si(111) double crystal, parallel monochromator
RadiationMonochromator: Si(111) double crystal, paralel monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→19 Å / Num. obs: 35799 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 23.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5190 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P6222 incomplete SeMAD model at 2.8 A resolution.

Resolution: 1.65→18.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.507 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19505 1729 4.8 %RANDOM
Rwork0.15741 ---
obs0.15926 34228 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--0.15 Å20 Å2
3---0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.094 Å0.092 Å
Refinement stepCycle: LAST / Resolution: 1.65→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 22 253 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222630
X-RAY DIFFRACTIONr_bond_other_d0.0010.021801
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9763575
X-RAY DIFFRACTIONr_angle_other_deg0.84934421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7545335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58825.203123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40815439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.354157
X-RAY DIFFRACTIONr_chiral_restr0.0930.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02513
X-RAY DIFFRACTIONr_mcbond_it1.91131598
X-RAY DIFFRACTIONr_mcbond_other0.5683657
X-RAY DIFFRACTIONr_mcangle_it3.05552572
X-RAY DIFFRACTIONr_scbond_it4.6981032
X-RAY DIFFRACTIONr_scangle_it6.80511993
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 117 -
Rwork0.251 2385 -
obs--96.19 %
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)
12.3955-1.1104-0.37326.3499.73914.37060.06880.54980.2922-0.52660.1845-0.2963-0.92520.222-0.25330.1649-0.0320.01610.1810.08190.153726.42828.2292.543
22.8501-0.8564-0.17617.772811.006614.1902-0.03410.46420.1938-0.52730.1121-0.0886-0.88290.1823-0.0780.2111-0.0089-0.00130.14210.07010.116224.79825.3814.973
31.8951-1.73291.93925.7496-1.61274.30390.310.3882-0.2635-0.3203-0.3587-0.05730.2222-0.00150.04870.1940.0463-0.05330.2629-0.06640.131920.8368.0740.194
47.8193-2.75058.9495.0746-10.134619.16880.3823-0.3402-0.0967-0.1450.22571.22220.0553-1.2184-0.6080.2195-0.1040.0560.1775-0.08950.576412.2635.5093.903
53.35190.25733.5923.75261.78775.7030.32960.2828-0.1422-0.2953-0.13590.02870.28050.0192-0.19370.20240.0274-0.03460.23110.01190.0818.33912.637-3.216
62.24830.59920.54681.90981.20764.103-0.01140.0370.2029-0.1428-0.0255-0.0816-0.30910.06560.03690.1163-0.001-0.01540.03080.03650.129626.93227.82917.506
70.79360.6264-0.42230.7687-0.27580.8593-0.0838-0.01460.061-0.1151-0.01530.005-0.0688-0.15810.09910.09880.0102-0.01140.07980.01070.087120.83721.1915.94
8-0.23341.8813-2.18664.3231-4.296923.2417-0.25660.24730.09560.0465-0.0597-0.0728-0.55380.65360.31630.1778-0.0472-0.0850.21820.06750.151312.94823.8730.402
91.8012-0.76342.56020.48560.36599.7173-0.1620.21090.1676-0.1388-0.03260.0515-0.17630.06250.19460.2155-0.0157-0.06540.19940.050.183311.224.64-7.172
102.3707-1.4512.18913.0864-0.71492.29570.23320.2075-0.0776-0.1968-0.1302-0.1227-0.0279-0.0395-0.1030.15520.0362-0.00520.1039-0.00580.093722.70812.8349.463
111.18090.13651.93550.83910.87213.3620.12880.2346-0.0116-0.2524-0.08670.04980.09050.0069-0.04210.19810.0534-0.02310.21490.02390.114117.54815.774-1.268
1219.28383.8315-4.0633-10.47247.88938.7269-0.45750.338-0.82820.58290.79260.37650.4837-0.6148-0.3350.34840.1114-0.07310.53460.13310.19089.78614.125-13.224
130.5402-0.34331.83050.6549-0.0118.8146-0.0620.20590.1369-0.1316-0.01130.0042-0.24670.1350.07330.1427-0.0211-0.05170.18370.04310.158115.65926.012-1.412
149.77853.99528.6672.4944-2.959928.77010.0735-0.260.55960.16370.10720.1538-0.154-1.2511-0.18070.08860.035-0.00860.16340.01270.172511.00723.64819.184
159.92822.43535.47981.47490.35959.1366-0.112-0.09950.33040.1789-0.04380.2081-0.4921-0.11990.15580.14870.02940.0170.1077-0.01850.175816.07628.86729.422
166.471-1.23687.00053.9373-6.663424.7558-0.2075-0.50160.51320.3012-0.2725-0.0574-1.0492-0.11090.480.17180.0121-0.03690.145-0.080.190220.88332.03333.007
17-2.03751.71937.102912.04382.441429.70270.04620.07920.18330.1558-0.0106-0.1247-0.3506-0.8867-0.03560.17880.0731-0.02530.1517-0.0030.231814.97932.8718.547
183.4312-0.3691-11.3973.95655.076145.8747-0.17420.40720.0297-0.121-0.13860.2486-0.8347-1.25910.31280.27630.0287-0.07350.13330.00340.182614.30632.6387.324
19-1.03121.5002-0.15717.36299.707427.1498-0.24540.40650.3113-0.27440.090.2267-0.69080.92740.15540.1134-0.1187-0.08050.44210.10770.20821.00329.662-4.481
207.9314-7.5143-4.543716.08455.384811.7721-0.51480.02190.241-0.43590.0098-0.6560.5361.63710.50490.16680.06450.00550.43250.0970.151423.95519.38-11.314
210.26330.04330.31190.1051-0.02030.4963-0.0030.04960.0189-0.0283-0.00430.0159-0.0308-0.0220.00730.14820.0013-0.00250.14150.00690.13518.154324.09224.6456
2214.5294-3.78626.587612.97642.3453.3018-0.3884-0.81440.30730.24360.5303-1.25170.0529-0.0976-0.14190.0290.0197-0.01720.21420.00310.068127.94112.90238.833
232.66586.53056.323514.425514.701317.3390.5656-0.1959-0.38030.3443-0.2872-0.5170.3355-0.4993-0.27840.0987-0.0376-0.03520.1060.05350.067228.0853.56728.275
240.4408-0.165-1.60864.55464.28047.18070.0722-0.22590.0308-0.0505-0.1281-0.3989-0.0395-0.29120.05580.026-0.00050.0140.1675-0.01790.088725.87611.32931.886
255.8771-4.7036.04743.1665-5.35913.3376-0.1112-0.12250.31390.18870.0455-0.2974-0.5456-0.03340.06570.102-0.0067-0.01240.1167-0.03450.151217.36425.23738.554
2625.52566.1184-1.53642.9332-8.864114.79270.3202-0.13261.21710.22520.27860.6842-0.1429-0.588-0.59880.05450.06920.0490.14130.02720.21438.62626.64429.703
274.8442-0.22330.86612.7217-3.10263.63060.2162-0.11240.05030.1946-0.00460.2815-0.0279-0.0535-0.21160.12010.01990.01280.1805-0.04710.100110.8522.54440.452
286.1860.0813-3.93574.54083.62484.51440.0208-0.36840.16140.2649-0.079-0.09910.13710.09060.05820.06180.0424-0.01370.12710.00170.054820.43517.11934.203
294.53-0.5911-0.56071.08281.75951.5715-0.1559-0.1427-0.3583-0.01870.00410.0558-0.01940.20690.15180.04660.01310.04310.05850.0670.08730.2629.81419.179
300.1656-0.71370.09531.2226-0.86991.9532-0.0752-0.04280.1398-0.188-0.01710.0048-0.0216-0.05490.09230.08240.0286-0.01160.02150.01140.081821.18714.03520.438
311.7149-0.2223.15790.9671-1.615111.180.0704-0.3197-0.16420.19290.0160.16310.3483-0.0683-0.08640.11740.02530.05990.17160.03160.080714.5826.69141.828
327.98910.19425.50825.9286-9.31211.63060.2265-0.333-0.3806-0.27220.08950.20791.0937-0.7824-0.3160.2108-0.0660.12060.2437-0.03740.10199.8976.80241.244
33-0.14010.4821-0.64262.2229-1.27982.30420.0012-0.14340.13090.0621-0.0912-0.0821-0.0157-0.0810.08990.0370.018-0.0110.0841-0.05260.118418.63919.8727.979
340.85240.019-1.08222.1501-1.34121.8557-0.0343-0.154-0.10880.27840.0440.2503-0.081-0.0476-0.00970.1188-0.00450.03810.2158-0.01520.105710.51715.74945.733
350.67360.18990.02870.9018-0.13369.3819-0.0082-0.236-0.05180.10530.00130.030.11260.00440.00690.03560.00870.01810.10720.02390.063517.9126.34634.747
364.48353.5086-1.30738.4816-0.912327.79730.07380.1121-0.12910.02570.0931-0.05890.7669-1.5416-0.16690.0633-0.0225-0.02490.11980.02160.005313.6838.61816.1
375.7279-1.0627-1.91673.85631.44882.0270.12050.2013-0.0828-0.6132-0.0964-0.0864-0.0256-0.0306-0.02410.17770.02960.01260.0555-0.0050.062923.954.9294.701
380.4849-0.8662-3.4832-0.37582.078910.87520.38860.250.3488-0.1390.42230.20970.1222-0.5286-0.81090.13510.0318-0.04050.14210.11620.17322.7542.94413.36
399.0317-0.0795.52811.21772.911.13770.0991-0.1589-0.53190.06040.0450.05230.0971-0.2659-0.14420.08210.00630.00960.05550.02040.089118.5720.28227.277
402.4103-0.1386-6.41536.93667.967913.7427-0.0847-0.20970.0040.3792-0.0546-0.10960.5469-0.03050.13930.080.012-0.00220.2530.00770.066123.265.86940.651
41-0.56381.13991.669921.41585.46527.0568-0.263-0.50330.65440.5513-0.2586-0.8078-0.30190.31440.52160.1058-0.0162-0.01820.2478-0.0010.17921.62516.41648.253
420.3684-0.1048-0.26390.32370.0360.5089-0.0068-0.056100.0265-0.00060.0060.02430.00040.00740.0972-0.0017-0.00720.12210.00690.104619.97810.193931.5319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 13
2X-RAY DIFFRACTION2A14 - 21
3X-RAY DIFFRACTION3A22 - 28
4X-RAY DIFFRACTION4A29 - 34
5X-RAY DIFFRACTION5A35 - 45
6X-RAY DIFFRACTION6A46 - 59
7X-RAY DIFFRACTION7A60 - 67
8X-RAY DIFFRACTION8A68 - 72
9X-RAY DIFFRACTION9A73 - 85
10X-RAY DIFFRACTION10A86 - 94
11X-RAY DIFFRACTION11A95 - 103
12X-RAY DIFFRACTION12A104 - 109
13X-RAY DIFFRACTION13A110 - 124
14X-RAY DIFFRACTION14A125 - 129
15X-RAY DIFFRACTION15A130 - 134
16X-RAY DIFFRACTION16A135 - 140
17X-RAY DIFFRACTION17A141 - 144
18X-RAY DIFFRACTION18A145 - 148
19X-RAY DIFFRACTION19A149 - 152
20X-RAY DIFFRACTION20A153 - 158
21X-RAY DIFFRACTION21A1001 - 1116
22X-RAY DIFFRACTION22B3 - 9
23X-RAY DIFFRACTION23B10 - 13
24X-RAY DIFFRACTION24B14 - 21
25X-RAY DIFFRACTION25B22 - 26
26X-RAY DIFFRACTION26B27 - 32
27X-RAY DIFFRACTION27B33 - 41
28X-RAY DIFFRACTION28B42 - 46
29X-RAY DIFFRACTION29B47 - 60
30X-RAY DIFFRACTION30B61 - 67
31X-RAY DIFFRACTION31B68 - 77
32X-RAY DIFFRACTION32B78 - 83
33X-RAY DIFFRACTION33B84 - 96
34X-RAY DIFFRACTION34B97 - 112
35X-RAY DIFFRACTION35B113 - 124
36X-RAY DIFFRACTION36B125 - 129
37X-RAY DIFFRACTION37B130 - 136
38X-RAY DIFFRACTION38B137 - 143
39X-RAY DIFFRACTION39B144 - 148
40X-RAY DIFFRACTION40B149 - 152
41X-RAY DIFFRACTION41B153 - 158
42X-RAY DIFFRACTION42B1001 - 1137

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