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- PDB-6dwf: Crystal structure of complex of BBKI mutant, L55R with Bovine Trypsin -

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Basic information

Entry
Database: PDB / ID: 6dwf
TitleCrystal structure of complex of BBKI mutant, L55R with Bovine Trypsin
Components
  • Cationic trypsin
  • Kunitz-type inihibitor
KeywordsHYDROLASE
Function / homology
Function and homology information


endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease 1 / Kunitz-type inihibitor
Similarity search - Component
Biological speciesBauhinia bauhinioides (plant)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLi, M. / Wlodawer, A. / Gustchina, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and modeling of kallikrein complexes.
Authors: Li, M. / Srp, J. / Gustchina, A. / Dauter, Z. / Mares, M. / Wlodawer, A.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cationic trypsin
G: Kunitz-type inihibitor
B: Cationic trypsin
C: Cationic trypsin
D: Cationic trypsin
E: Cationic trypsin
F: Cationic trypsin
H: Kunitz-type inihibitor
I: Kunitz-type inihibitor
J: Kunitz-type inihibitor
K: Kunitz-type inihibitor
L: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)252,21912
Polymers252,21912
Non-polymers00
Water29,4731636
1
A: Cationic trypsin
G: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)42,0362
Polymers42,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-9 kcal/mol
Surface area15180 Å2
MethodPISA
2
B: Cationic trypsin
H: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)42,0362
Polymers42,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-9 kcal/mol
Surface area15130 Å2
MethodPISA
3
C: Cationic trypsin
I: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)42,0362
Polymers42,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-9 kcal/mol
Surface area15190 Å2
MethodPISA
4
D: Cationic trypsin
J: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)42,0362
Polymers42,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-9 kcal/mol
Surface area15170 Å2
MethodPISA
5
E: Cationic trypsin
K: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)42,0362
Polymers42,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-8 kcal/mol
Surface area15180 Å2
MethodPISA
6
F: Cationic trypsin
L: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)42,0362
Polymers42,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-9 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.303, 207.303, 107.167
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16G
26H
17G
27I
18G
28J
19G
29K
110G
210L
111B
211C
112B
212D
113B
213E
114B
214F
115C
215D
116C
216E
117C
217F
118D
218E
119D
219F
120E
220F
121H
221I
122H
222J
123H
223K
124H
224L
125I
225J
126I
226K
127I
227L
128J
228K
129J
229L
130K
230L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEASNASNAA16 - 2451 - 223
21ILEILEASNASNBC16 - 2451 - 223
12ILEILEASNASNAA16 - 2451 - 223
22ILEILEASNASNCD16 - 2451 - 223
13ILEILEASNASNAA16 - 2451 - 223
23ILEILEASNASNDE16 - 2451 - 223
14ILEILEASNASNAA16 - 2451 - 223
24ILEILEASNASNEF16 - 2451 - 223
15ILEILEASNASNAA16 - 2451 - 223
25ILEILEASNASNFG16 - 2451 - 223
16SERSERTHRTHRGB1 - 1637 - 169
26SERSERTHRTHRHH1 - 1637 - 169
17SERSERTHRTHRGB1 - 1637 - 169
27SERSERTHRTHRII1 - 1637 - 169
18SERSERTHRTHRGB1 - 1637 - 169
28SERSERTHRTHRJJ1 - 1637 - 169
19SERSERTHRTHRGB1 - 1637 - 169
29SERSERTHRTHRKK1 - 1637 - 169
110SERSERTHRTHRGB1 - 1637 - 169
210SERSERTHRTHRLL1 - 1637 - 169
111ILEILEASNASNBC16 - 2451 - 223
211ILEILEASNASNCD16 - 2451 - 223
112ILEILEASNASNBC16 - 2451 - 223
212ILEILEASNASNDE16 - 2451 - 223
113ILEILEASNASNBC16 - 2451 - 223
213ILEILEASNASNEF16 - 2451 - 223
114ILEILEASNASNBC16 - 2451 - 223
214ILEILEASNASNFG16 - 2451 - 223
115ILEILEASNASNCD16 - 2451 - 223
215ILEILEASNASNDE16 - 2451 - 223
116ILEILEASNASNCD16 - 2451 - 223
216ILEILEASNASNEF16 - 2451 - 223
117ILEILEASNASNCD16 - 2451 - 223
217ILEILEASNASNFG16 - 2451 - 223
118ILEILEASNASNDE16 - 2451 - 223
218ILEILEASNASNEF16 - 2451 - 223
119ILEILEASNASNDE16 - 2451 - 223
219ILEILEASNASNFG16 - 2451 - 223
120ILEILEASNASNEF16 - 2451 - 223
220ILEILEASNASNFG16 - 2451 - 223
121SERSERTHRTHRHH1 - 1637 - 169
221SERSERTHRTHRII1 - 1637 - 169
122SERSERTHRTHRHH1 - 1637 - 169
222SERSERTHRTHRJJ1 - 1637 - 169
123SERSERTHRTHRHH1 - 1637 - 169
223SERSERTHRTHRKK1 - 1637 - 169
124SERSERTHRTHRHH1 - 1637 - 169
224SERSERTHRTHRLL1 - 1637 - 169
125SERSERTHRTHRII1 - 1637 - 169
225SERSERTHRTHRJJ1 - 1637 - 169
126SERSERTHRTHRII1 - 1637 - 169
226SERSERTHRTHRKK1 - 1637 - 169
127SERSERTHRTHRII1 - 1637 - 169
227SERSERTHRTHRLL1 - 1637 - 169
128SERSERTHRTHRJJ1 - 1637 - 169
228SERSERTHRTHRKK1 - 1637 - 169
129SERSERTHRTHRJJ1 - 1637 - 169
229SERSERTHRTHRLL1 - 1637 - 169
130SERSERTHRTHRKK1 - 1637 - 169
230SERSERTHRTHRLL1 - 1637 - 169

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

#1: Protein
Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 6 / Fragment: residues 24-246 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein
Kunitz-type inihibitor


Mass: 18712.182 Da / Num. of mol.: 6 / Fragment: residues 19-181 / Mutation: L55R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bauhinia bauhinioides (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VEQ7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1636 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.6M Ammonium Sulfate, 0.1M Sodium Citrate at pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.492
11-K, -H, -L20.508
ReflectionResolution: 1.94→50 Å / Num. obs: 189147 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / CC1/2: 0.9545 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.024 / Rrim(I) all: 0.081 / Rsym value: 0.077 / Net I/σ(I): 26.5
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 1.183 / Num. unique all: 15175 / Num. unique obs: 7121 / Rpim(I) all: 0.795 / Rrim(I) all: 1.412 / Rsym value: 1.151 / % possible all: 74.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NA1
Resolution: 1.94→49.79 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.825 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22294 1622 1 %RANDOM
Rwork0.19636 ---
obs0.19662 168232 88.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0 Å2
2---0.52 Å2-0 Å2
3---1.04 Å2
Refinement stepCycle: 1 / Resolution: 1.94→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17352 0 0 1636 18988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01917790
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216224
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.95524114
X-RAY DIFFRACTIONr_angle_other_deg1.139337902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82752286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10424.87690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.707152910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6961560
X-RAY DIFFRACTIONr_chiral_restr0.0840.22688
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023348
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1691.5229234
X-RAY DIFFRACTIONr_mcbond_other1.1681.5229233
X-RAY DIFFRACTIONr_mcangle_it2.1092.27711472
X-RAY DIFFRACTIONr_mcangle_other2.1092.27711473
X-RAY DIFFRACTIONr_scbond_it0.9291.6328555
X-RAY DIFFRACTIONr_scbond_other0.9291.6328556
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6212.40312636
X-RAY DIFFRACTIONr_long_range_B_refined5.42718.74619771
X-RAY DIFFRACTIONr_long_range_B_other5.42618.74819772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A139320.01
12B139320.01
21A139340.03
22C139340.03
31A139420.02
32D139420.02
41A139500.01
42E139500.01
51A139180.02
52F139180.02
61G101180.02
62H101180.02
71G101380.02
72I101380.02
81G101020.02
82J101020.02
91G101240.02
92K101240.02
101G101280.02
102L101280.02
111B139280.02
112C139280.02
121B139780
122D139780
131B139460.01
132E139460.01
141B139760.01
142F139760.01
151C139500.02
152D139500.02
161C139560.02
162E139560.02
171C139400.02
172F139400.02
181D139540.01
182E139540.01
191D139880
192F139880
201E139380.01
202F139380.01
211H101160.02
212I101160.02
221H101240.02
222J101240.02
231H100860.02
232K100860.02
241H101500.02
242L101500.02
251I100920.02
252J100920.02
261I101160.02
262K101160.02
271I101200.02
272L101200.02
281J101080.02
282K101080.02
291J101220.02
292L101220.02
301K100900.02
302L100900.02
LS refinement shellResolution: 1.943→1.994 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 4 -
Rwork0.266 332 -
obs--2.36 %
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)
10.67480.37450.11060.6825-0.16530.4992-0.1033-0.11260.048-0.15810.0460.07380.06870.00360.05730.1165-0.00880.04090.06120.01520.074791.510884.40280.7363
20.82440.53240.41723.3911-0.21260.56780.20130.0003-0.1222-0.0741-0.2366-0.20230.0720.00210.03530.1018-0.012-0.01440.073-0.03410.0673130.840460.931687.1032
31.00770.4458-0.20350.58430.16940.4524-0.1413-0.12480.0248-0.19210.0618-0.0174-0.07320.00560.07950.1436-0.0289-0.04470.0925-0.04560.0712115.84535.621580.723
40.5710.2394-0.15492.23380.16160.35080.14680.01970.0576-0.0626-0.13720.1536-0.03370.0009-0.00960.1042-0.02630.00310.05750.02110.056776.723159.021387.0571
50.20550.46610.21841.62250.22120.80030.1303-0.08760.02370.1814-0.2487-0.0360.068-0.08670.11840.1254-0.04330.02290.0964-0.04250.050627.24691.868585.4658
61.72991.72850.34852.7441-0.38250.9822-0.0734-0.12630.218-0.20010.06990.23710.0229-0.04160.00350.0794-0.03650.00620.0869-0.02110.0335-12.703923.661779.1517
70.68590.2093-0.12981.57360.41950.3315-0.0668-0.08990.0541-0.07550.1042-0.05870.01830.0603-0.03740.1067-0.00170.01990.03460.00120.0399112.4596106.923882.0236
81.4250.8974-0.75421.4685-0.55140.8980.0930.01660.15150.096-0.0522-0.0516-0.0490.0046-0.04080.0502-0.0178-0.00280.06140.00160.094139.79990.218585.008
90.7720.31880.07171.7593-0.58110.5149-0.1176-0.1067-0.0929-0.07790.13810.06050.0255-0.033-0.02050.11020.0014-0.00480.06190.00420.072395.051913.012182.3477
101.17670.72590.69440.83940.5560.98970.11520.0024-0.09190.155-0.0492-0.01530.0379-0.0118-0.0660.0455-0.02880.00040.04930.00580.07867.617929.761484.6691
111.24860.4868-0.151.3258-0.07310.0450.07060.0310.05040.029-0.0851-0.12070.0277-0.03170.01450.0579-0.04490.020.1041-0.010.033136.372331.212784.2793
120.62160.55090.12582.09010.39440.6469-0.07440.04970.0534-0.07330.0509-0.0523-0.0182-0.02470.02360.09-0.0117-0.00240.00710.00310.03097.975846.237381.6604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 245
2X-RAY DIFFRACTION2B16 - 245
3X-RAY DIFFRACTION3C16 - 245
4X-RAY DIFFRACTION4D16 - 245
5X-RAY DIFFRACTION5E16 - 245
6X-RAY DIFFRACTION6F16 - 245
7X-RAY DIFFRACTION7G1 - 163
8X-RAY DIFFRACTION8H1 - 163
9X-RAY DIFFRACTION9I1 - 163
10X-RAY DIFFRACTION10J1 - 163
11X-RAY DIFFRACTION11K1 - 163
12X-RAY DIFFRACTION12L1 - 163

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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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