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- PDB-4bww: Crystal structure of spin labelled azurin T21R1. -

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Basic information

Entry
Database: PDB / ID: 4bww
TitleCrystal structure of spin labelled azurin T21R1.
ComponentsAZURIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


transition metal ion binding / electron transfer activity / periplasmic space / copper ion binding / zinc ion binding / identical protein binding
Similarity search - Function
Azurin / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / NITRATE ION / Azurin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsHagelueken, G.
CitationJournal: Bmc Struct.Biol. / Year: 2014
Title: High-Resolution Crystal Structure of Spin Labelled (T21R1) Azurin from Pseudomonas Aeruginosa: A Challenging Structural Benchmark for in Silico Spin Labelling Algorithms.
Authors: Florin, N. / Schiemann, O. / Hagelueken, G.
History
DepositionJul 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AZURIN
B: AZURIN
C: AZURIN
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,41126
Polymers57,6304
Non-polymers1,78122
Water8,809489
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-85.2 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.950, 53.660, 73.210
Angle α, β, γ (deg.)74.40, 89.33, 83.41
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
AZURIN /


Mass: 14407.444 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MTSSL SPIN LABEL ATTACHED TO CYSTEINE INTRODUCED AT POSITION 21
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PEHISGSTTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: P00282

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Non-polymers , 5 types, 511 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCYS INTRODUCED AT POSITION 21 OF NATIVE PROTEIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 2.14 M AMMONIUM SULFATE, 0.28 M AMMONIUM NITRATE, 0.1 M SODIUM CACODYLATE PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.5→51.3 Å / Num. obs: 82307 / % possible obs: 91.8 % / Observed criterion σ(I): 1.1 / Redundancy: 1.9 % / Biso Wilson estimate: 14.25 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.5
Reflection shellHighest resolution: 1.48 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.1 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E67
Resolution: 1.48→48.123 Å / SU ML: 0.21 / σ(F): 1.96 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 1999 2.4 %
Rwork0.1794 --
obs0.1802 82294 91.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→48.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 97 489 4526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094191
X-RAY DIFFRACTIONf_angle_d1.2585668
X-RAY DIFFRACTIONf_dihedral_angle_d21.6451641
X-RAY DIFFRACTIONf_chiral_restr0.08617
X-RAY DIFFRACTIONf_plane_restr0.005731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5170.39561390.355581X-RAY DIFFRACTION91
1.517-1.5580.3291430.31995745X-RAY DIFFRACTION91
1.558-1.60390.29661410.28825645X-RAY DIFFRACTION90
1.6039-1.65570.27541370.27455524X-RAY DIFFRACTION89
1.6557-1.71480.29871400.25065639X-RAY DIFFRACTION90
1.7148-1.78350.25291450.22825796X-RAY DIFFRACTION92
1.7835-1.86470.23381440.21395767X-RAY DIFFRACTION92
1.8647-1.9630.22941400.18845649X-RAY DIFFRACTION90
1.963-2.0860.20841390.16655634X-RAY DIFFRACTION90
2.086-2.2470.19821450.16035788X-RAY DIFFRACTION93
2.247-2.47310.19861460.16095877X-RAY DIFFRACTION93
2.4731-2.8310.17411450.15565819X-RAY DIFFRACTION93
2.831-3.56660.16121470.14795904X-RAY DIFFRACTION95
3.5666-48.14890.18941480.14075927X-RAY DIFFRACTION95
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)
12.59771.15762.64725.2761-0.00923.2108-0.08131.1709-0.3475-0.59990.5001-0.15350.3010.7934-0.38480.1966-0.01110.00090.283-0.07120.168446.411-39.49883.6247
24.3673-3.8632.98395.3718-0.90414.99370.02560.27050.0817-0.2251-0.0807-0.2479-0.01390.35290.08110.1003-0.03150.01760.1570.01130.138652.8156-29.12313.1506
36.16542.52065.09614.29843.79565.1298-0.54270.49540.2401-1.24820.41820.456-0.31630.12310.08920.334-0.0222-0.09860.2197-0.01340.196336.7639-36.67350.7702
41.9663-0.44631.80111.08770.37982.50790.070.0307-0.1662-0.1468-0.0017-0.12610.10210.0242-0.05830.0626-0.0053-0.00260.1405-0.01060.126450.3523-37.806115.9875
51.7228-1.7695-0.35453.1296-1.57493.93520.0101-0.09610.15730.12490.09440.0283-0.26970.0977-0.04330.0463-0.0153-0.01690.1435-0.02020.131237.4776-30.057722.219
67.4715-0.00094.25584.94150.67313.46150.298-0.8499-0.61930.3445-0.18350.03280.17370.0996-0.09720.1485-0.0283-0.02820.26380.07690.157742.7686-38.346828.4093
76.115-0.5438-0.79362.77030.01371.905-0.0129-0.1788-0.44610.0211-0.0090.03250.10420.0840.01920.0677-0.0162-0.02970.11040.0080.106342.5926-39.721620.0023
86.3991-1.08571.81585.51180.55752.86920.01070.0819-0.1208-0.4029-0.01470.6222-0.1903-0.2504-0.0550.1845-0.0035-0.05670.1472-0.00860.149434.9015-38.73669.2815
93.9240.50062.00422.67630.02833.0049-0.0601-0.04860.0547-0.20470.0610.1526-0.14280.00910.02280.05740.0154-0.01370.1225-0.01180.126842.056-29.54314.1911
107.24272.9779-3.20553.16581.28584.9408-0.13320.19570.49460.12390.67111.5245-0.7407-0.266-0.67610.26210.0250.02740.150.06390.277132.8968-2.8846-1.1372
111.49-0.49880.59412.5996-0.73412.0753-0.1158-0.0958-0.10990.18520.23440.3678-0.0997-0.0867-0.11620.18350.02260.05450.11330.02530.142135.7341-10.31862.9685
121.3956-0.39970.11622.6703-1.06912.1756-0.1393-0.15390.01040.63970.0775-0.1888-0.22130.05710.04820.2658-0.0014-0.03020.12090.00440.09647.9463-12.96838.0452
134.2421-0.6971-3.65923.5318-0.14638.0457-0.25120.01260.09830.19590.1139-0.0733-0.08430.26620.10140.2521-0.0458-0.0370.1459-0.00060.110545.4635-2.8808-3.0022
141.77030.5428-0.22715.4316-4.645.2508-0.09260.0264-0.0483-0.14120.19040.14070.0438-0.0142-0.12510.1665-0.0080.01620.1122-0.01020.090442.257-14.6983-0.8638
150.5881.74071.13566.93074.6863.18150.232-0.0117-0.1660.82710.403-0.79070.34651.0861-0.6830.2756-0.0453-0.08310.2721-0.03190.18669.2804-17.011242.3339
161.98830.0291-2.23232.6182-1.10862.9535-0.01240.0656-0.01590.0115-0.073-0.0214-0.0470.22590.12070.17320.0209-0.0340.1756-0.0080.149263.2559-27.038432.4349
172.53911.99371.45094.35215.18128.04090.0371-0.2784-0.00381.03520.1104-0.27840.17260.1058-0.20410.3898-0.0486-0.06370.197-0.00340.169765.4886-17.964351.9669
181.28170.2070.91313.08713.34688.4310.02480.04440.0493-0.09670.1665-0.1276-0.59740.4933-0.21730.1645-0.0517-0.0110.13570.0070.109964.0499-16.46934.1301
191.83221.50133.00241.11892.06578.5866-0.12370.03650.2049-0.0709-0.09430.12230.0552-0.14920.20730.17790.0012-0.04660.156-0.01790.160156.8953-20.090828.775
203.30640.06323.12274.192-1.61075.38280.15990.3489-0.5696-0.00640.02710.51550.2338-0.6292-0.19220.09310.0165-0.00460.2475-0.06680.229447.41-22.467739.8434
215.0849-0.90550.31156.58440.1930.03430.04420.40550.3248-1.0981-0.2260.4993-1.1774-0.62870.00780.41760.1641-0.12210.3162-0.0080.263347.0023-14.571230.664
228.2097-0.0648-3.24144.81560.99416.40910.1184-0.19780.29690.191-0.03570.3935-0.7171-0.2016-0.0910.21210.0502-0.01950.1253-0.02440.16650.8003-13.63740.1644
231.9593-0.7252-0.3314.69942.05617.9870.09250.03490.1219-0.2128-0.0372-0.0348-0.80380.1029-0.0410.2101-0.0118-0.02620.13360.00240.130860.4585-12.538438.2085
244.3226-0.3706-1.34092.43070.84428.51290.1326-0.3806-0.22761.0744-0.05910.08810.4215-0.0315-0.07180.3982-0.07740.02490.18050.02870.16655.2689-22.401949.8342
254.0415-1.3986-0.84315.25051.11871.92020.10930.2002-0.1404-0.1201-0.20470.39740.3136-0.23970.06440.1716-0.0034-0.04510.1679-0.03690.131853.9455-25.960632.2683
266.53291.64721.87079.44315.8193.90910.0892-0.37490.12510.53250.1243-0.43850.13180.3629-0.28220.2688-0.0239-0.02160.14030.01160.145960.8194-23.882948.9568
273.7858-4.8392-0.70436.24591.09770.6494-0.2441-0.4399-0.5461.02380.5180.94650.2518-0.1697-0.43770.3914-0.0530.02010.1910.04620.26558.2899-50.633159.0372
288.9925-4.49994.87893.7861-1.8774.7885-0.0438-0.24580.21510.34610.12090.1146-0.3689-0.2668-0.01780.2672-0.01770.08330.14180.02410.180257.112-35.891855.8871
292.90260.6305-0.69696.8235.0994.3030.1933-0.0631-0.51-0.0454-0.0132-0.14540.70310.0767-0.18290.3102-0.016-0.07210.13640.01530.178868.3271-54.998859.1138
301.2985-1.94460.51553.1045-0.66491.02630.17150.107-0.1179-0.17260.00860.3350.1257-0.1369-0.17220.2279-0.01960.00310.12190.01240.150557.2147-42.31548.8383
315.9605-2.38680.30525.8545-2.52921.86350.08170.1940.6692-0.4865-0.428-0.0432-0.0720.4135-0.06530.40550.0710.05710.13520.03450.142765.5489-36.738238.9721
322.29550.74860.70846.13411.36144.4590.64950.7352-0.4044-0.8712-0.54230.7070.796-0.03920.21790.53910.0353-0.15850.1668-0.0680.177957.6257-41.417336.2115
333.7815-3.5545-1.92654.58980.10243.53260.50780.4446-0.6853-1.2293-0.3160.46450.82940.16280.5760.52780.1263-0.01340.1584-0.06540.058663.9154-47.824340.9266
346.2757-4.91612.95278.6495-2.13031.79340.3967-0.0658-0.6154-0.3462-0.07020.91880.2653-0.0694-0.28530.2949-0.0425-0.04440.1427-0.0110.183956.9855-49.81948.3526
356.2292-3.45640.7816.8556-1.48696.44180.10250.00530.1059-0.1271-0.2165-0.61840.15360.61220.06950.2048-0.0106-0.00090.16910.03020.159672.7412-46.916851.3271
362.8218-2.60451.77085.4511-1.90082.35410.02680.04030.04190.2416-0.0596-0.0765-0.10430.1090.07450.1996-0.02180.0120.130.00290.105464.611-39.267550.6862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 8 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 9 THROUGH 18 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 19 THROUGH 27 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 28 THROUGH 48 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 49 THROUGH 66 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 67 THROUGH 75 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 76 THROUGH 91 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 92 THROUGH 107 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 108 THROUGH 128 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 1 THROUGH 8 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 9 THROUGH 48 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 49 THROUGH 91 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 92 THROUGH 107 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 108 THROUGH 128 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 1 THROUGH 8 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 9 THROUGH 18 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 19 THROUGH 27 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 28 THROUGH 40 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 41 THROUGH 48 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 49 THROUGH 66 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 67 THROUGH 75 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 76 THROUGH 85 )
23X-RAY DIFFRACTION23CHAIN C AND (RESID 86 THROUGH 101 )
24X-RAY DIFFRACTION24CHAIN C AND (RESID 102 THROUGH 111 )
25X-RAY DIFFRACTION25CHAIN C AND (RESID 112 THROUGH 121 )
26X-RAY DIFFRACTION26CHAIN C AND (RESID 122 THROUGH 128 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 1 THROUGH 8 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 9 THROUGH 18 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 19 THROUGH 27 )
30X-RAY DIFFRACTION30CHAIN D AND (RESID 28 THROUGH 55 )
31X-RAY DIFFRACTION31CHAIN D AND (RESID 56 THROUGH 66 )
32X-RAY DIFFRACTION32CHAIN D AND (RESID 67 THROUGH 75 )
33X-RAY DIFFRACTION33CHAIN D AND (RESID 76 THROUGH 85 )
34X-RAY DIFFRACTION34CHAIN D AND (RESID 86 THROUGH 101 )
35X-RAY DIFFRACTION35CHAIN D AND (RESID 102 THROUGH 111 )
36X-RAY DIFFRACTION36CHAIN D AND (RESID 112 THROUGH 128 )

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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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