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- PDB-6nd9: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH CALCIUM -

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Basic information

Entry
Database: PDB / ID: 6nd9
TitleRHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH CALCIUM
Components
  • (Snaclec rhodocetin subunit ...) x 2
  • Integrin alpha-2
KeywordsCELL ADHESION/TOXIN / C-TYPE LECTIN / INTEGRIN / VENOM / COAGULATION / CELL ADHESION / CELL ADHESION-TOXIN complex
Function / homology
Function and homology information


collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / positive regulation of cell projection organization / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / skin morphogenesis ...collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / positive regulation of cell projection organization / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / skin morphogenesis / CHL1 interactions / positive regulation of smooth muscle contraction / response to L-ascorbic acid / collagen-activated signaling pathway / basal part of cell / Laminin interactions / positive regulation of phagocytosis, engulfment / Platelet Adhesion to exposed collagen / hepatocyte differentiation / focal adhesion assembly / mammary gland development / heparan sulfate proteoglycan binding / mesodermal cell differentiation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / response to amine / integrin complex / positive regulation of smooth muscle cell migration / MET activates PTK2 signaling / cell adhesion mediated by integrin / Syndecan interactions / response to muscle activity / cell-substrate adhesion / positive regulation of collagen biosynthetic process / positive regulation of epithelial cell migration / ECM proteoglycans / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / collagen binding / laminin binding / extracellular matrix organization / positive regulation of smooth muscle cell proliferation / positive regulation of cell adhesion / axon terminus / animal organ morphogenesis / cell-matrix adhesion / positive regulation of translation / integrin-mediated signaling pathway / cellular response to estradiol stimulus / female pregnancy / cellular response to mechanical stimulus / cell-cell adhesion / integrin binding / blood coagulation / amyloid-beta binding / toxin activity / virus receptor activity / response to hypoxia / cell adhesion / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / : / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / C-type lectin, conserved site / C-type lectin domain signature. / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor ...: / : / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / C-type lectin, conserved site / C-type lectin domain signature. / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Snaclec rhodocetin subunit gamma / Snaclec rhodocetin subunit delta / Integrin alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Calloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsStetefeld, J. / McDougall, M.D. / Loewen, P.C.
CitationJournal: To be published
Title: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CALCIUM
Authors: Stetefeld, J. / McDougall, M.D. / Loewen, P.C.
History
DepositionDec 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Snaclec rhodocetin subunit gamma
B: Snaclec rhodocetin subunit delta
C: Integrin alpha-2
D: Snaclec rhodocetin subunit gamma
E: Snaclec rhodocetin subunit delta
F: Integrin alpha-2
G: Snaclec rhodocetin subunit gamma
H: Snaclec rhodocetin subunit delta
I: Integrin alpha-2
J: Snaclec rhodocetin subunit gamma
K: Snaclec rhodocetin subunit delta
L: Integrin alpha-2
M: Snaclec rhodocetin subunit gamma
N: Snaclec rhodocetin subunit delta
O: Integrin alpha-2
P: Snaclec rhodocetin subunit gamma
Q: Snaclec rhodocetin subunit delta
R: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,33251
Polymers326,13118
Non-polymers2,20133
Water18010
1
A: Snaclec rhodocetin subunit gamma
B: Snaclec rhodocetin subunit delta
C: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8039
Polymers54,3553
Non-polymers4476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Snaclec rhodocetin subunit gamma
E: Snaclec rhodocetin subunit delta
F: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,76010
Polymers54,3553
Non-polymers4057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Snaclec rhodocetin subunit gamma
H: Snaclec rhodocetin subunit delta
I: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7429
Polymers54,3553
Non-polymers3876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Snaclec rhodocetin subunit gamma
K: Snaclec rhodocetin subunit delta
L: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7389
Polymers54,3553
Non-polymers3836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Snaclec rhodocetin subunit gamma
N: Snaclec rhodocetin subunit delta
O: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6107
Polymers54,3553
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Snaclec rhodocetin subunit gamma
Q: Snaclec rhodocetin subunit delta
R: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6807
Polymers54,3553
Non-polymers3244
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.044, 131.044, 251.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22G
13A
23J
14A
24M
15A
25P
16B
26E
17B
27H
18B
28K
19B
29N
110B
210Q
111C
211F
112C
212I
113C
213L
114C
214O
115C
215R
116D
216G
117D
217J
118D
218M
119D
219P
120E
220H
121E
221K
122E
222N
123E
223Q
124F
224I
125F
225L
126F
226O
127F
227R
128G
228J
129G
229M
130G
230P
131H
231K
132H
232N
133H
233Q
134I
234L
135I
235O
136I
236R
137J
237M
138J
238P
139K
239N
140K
240Q
141L
241O
142L
242R
143M
243P
144N
244Q
145O
245R

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSERAA3 - 1333 - 133
21ASNASNSERSERDD3 - 1333 - 133
12ASNASNSERSERAA3 - 1333 - 133
22ASNASNSERSERGG3 - 1333 - 133
13ASNASNSERSERAA3 - 1333 - 133
23ASNASNSERSERJJ3 - 1333 - 133
14ASNASNSERSERAA3 - 1333 - 133
24ASNASNSERSERMM3 - 1333 - 133
15ASNASNSERSERAA3 - 1333 - 133
25ASNASNSERSERPP3 - 1333 - 133
16CYSCYSPHEPHEBB1 - 1221 - 122
26CYSCYSPHEPHEEE1 - 1221 - 122
17CYSCYSPHEPHEBB1 - 1221 - 122
27CYSCYSPHEPHEHH1 - 1221 - 122
18CYSCYSPHEPHEBB1 - 1221 - 122
28CYSCYSPHEPHEKK1 - 1221 - 122
19CYSCYSPHEPHEBB1 - 1221 - 122
29CYSCYSPHEPHENN1 - 1221 - 122
110CYSCYSPHEPHEBB1 - 1221 - 122
210CYSCYSPHEPHEQQ1 - 1221 - 122
111LEULEUPHEPHECC172 - 36223 - 213
211LEULEUPHEPHEFF172 - 36223 - 213
112LEULEUPHEPHECC172 - 36223 - 213
212LEULEUPHEPHEII172 - 36223 - 213
113LEULEUPHEPHECC172 - 36223 - 213
213LEULEUPHEPHELL172 - 36223 - 213
114LEULEUPHEPHECC172 - 36223 - 213
214LEULEUPHEPHEOO172 - 36223 - 213
115LEULEUPHEPHECC172 - 36223 - 213
215LEULEUPHEPHERR172 - 36223 - 213
116ASNASNSERSERDD3 - 1333 - 133
216ASNASNSERSERGG3 - 1333 - 133
117ASNASNSERSERDD3 - 1333 - 133
217ASNASNSERSERJJ3 - 1333 - 133
118ASNASNSERSERDD3 - 1333 - 133
218ASNASNSERSERMM3 - 1333 - 133
119ASNASNSERSERDD3 - 1333 - 133
219ASNASNSERSERPP3 - 1333 - 133
120CYSCYSPHEPHEEE1 - 1221 - 122
220CYSCYSPHEPHEHH1 - 1221 - 122
121CYSCYSPHEPHEEE1 - 1221 - 122
221CYSCYSPHEPHEKK1 - 1221 - 122
122CYSCYSPHEPHEEE1 - 1221 - 122
222CYSCYSPHEPHENN1 - 1221 - 122
123CYSCYSPHEPHEEE1 - 1221 - 122
223CYSCYSPHEPHEQQ1 - 1221 - 122
124LEULEUPHEPHEFF172 - 36223 - 213
224LEULEUPHEPHEII172 - 36223 - 213
125LEULEUPHEPHEFF172 - 36223 - 213
225LEULEUPHEPHELL172 - 36223 - 213
126LEULEUPHEPHEFF172 - 36223 - 213
226LEULEUPHEPHEOO172 - 36223 - 213
127LEULEUPHEPHEFF172 - 36223 - 213
227LEULEUPHEPHERR172 - 36223 - 213
128ASNASNSERSERGG3 - 1333 - 133
228ASNASNSERSERJJ3 - 1333 - 133
129ASNASNSERSERGG3 - 1333 - 133
229ASNASNSERSERMM3 - 1333 - 133
130ASNASNSERSERGG3 - 1333 - 133
230ASNASNSERSERPP3 - 1333 - 133
131CYSCYSPHEPHEHH1 - 1221 - 122
231CYSCYSPHEPHEKK1 - 1221 - 122
132CYSCYSPHEPHEHH1 - 1221 - 122
232CYSCYSPHEPHENN1 - 1221 - 122
133CYSCYSPHEPHEHH1 - 1221 - 122
233CYSCYSPHEPHEQQ1 - 1221 - 122
134LEULEUPHEPHEII172 - 36223 - 213
234LEULEUPHEPHELL172 - 36223 - 213
135LEULEUPHEPHEII172 - 36223 - 213
235LEULEUPHEPHEOO172 - 36223 - 213
136LEULEUPHEPHEII172 - 36223 - 213
236LEULEUPHEPHERR172 - 36223 - 213
137ASNASNSERSERJJ3 - 1333 - 133
237ASNASNSERSERMM3 - 1333 - 133
138ASNASNSERSERJJ3 - 1333 - 133
238ASNASNSERSERPP3 - 1333 - 133
139CYSCYSPHEPHEKK1 - 1221 - 122
239CYSCYSPHEPHENN1 - 1221 - 122
140CYSCYSPHEPHEKK1 - 1221 - 122
240CYSCYSPHEPHEQQ1 - 1221 - 122
141LEULEUPHEPHELL172 - 36223 - 213
241LEULEUPHEPHEOO172 - 36223 - 213
142LEULEUPHEPHELL172 - 36223 - 213
242LEULEUPHEPHERR172 - 36223 - 213
143ASNASNSERSERMM3 - 1333 - 133
243ASNASNSERSERPP3 - 1333 - 133
144CYSCYSPHEPHENN1 - 1221 - 122
244CYSCYSPHEPHEQQ1 - 1221 - 122
145LEULEUPHEPHEOO172 - 36223 - 213
245LEULEUPHEPHERR172 - 36223 - 213

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
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

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Snaclec rhodocetin subunit ... , 2 types, 12 molecules ADGJMPBEHKNQ

#1: Protein
Snaclec rhodocetin subunit gamma


Mass: 15741.510 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: D2YW39
#2: Protein
Snaclec rhodocetin subunit delta


Mass: 14875.982 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: D2YW40

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Protein , 1 types, 6 molecules CFILOR

#3: Protein
Integrin alpha-2 / CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / ...CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / VLA-2 subunit alpha


Mass: 23737.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2, CD49B / Production host: Escherichia coli (E. coli) / References: UniProt: P17301

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Non-polymers , 7 types, 43 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.54 Å3/Da / Density % sol: 65.23 % / Mosaicity: 0.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M TRIS, 2.65 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 27, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→131.044 Å / Num. obs: 93403 / % possible obs: 100 % / Redundancy: 6.4 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.124 / Rsym value: 0.114 / Net I/av σ(I): 6.5 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.9-3.066.40.61.3136230.2580.6540.6100
3.06-3.246.40.3762.1128890.1610.4090.376100
3.24-3.476.40.2353.3121120.1010.2560.235100
3.47-3.746.40.1485.2112830.0630.1610.148100
3.74-4.16.40.1057.3104030.0450.1140.105100
4.1-4.596.40.0741093860.0320.080.074100
4.59-5.296.40.06611.182850.0280.0720.066100
5.29-6.486.50.0731070220.0310.080.073100
6.48-9.176.50.04514.554240.0190.0490.04599.9
9.17-48.0166.30.0292129760.0120.0320.02999.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMAC5.8.0238phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5THP

5thp


Resolution: 2.9→48.06 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.873 / SU B: 17.424 / SU ML: 0.324 / SU R Cruickshank DPI: 2.0364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.036 / ESU R Free: 0.396 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.272 4578 4.9 %RANDOM
Rwork0.2292 ---
obs0.2313 88792 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 178.73 Å2 / Biso mean: 49.621 Å2 / Biso min: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 2.9→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21486 0 107 10 21603
Biso mean--73.43 22.92 -
Num. residues----2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01322142
X-RAY DIFFRACTIONr_bond_other_d0.0010.01819680
X-RAY DIFFRACTIONr_angle_refined_deg1.391.63730010
X-RAY DIFFRACTIONr_angle_other_deg1.2071.57945646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.58652646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01222.4631218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.951153708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.25315132
X-RAY DIFFRACTIONr_chiral_restr0.0520.22766
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025028
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41040.08
12D41040.08
21A40950.08
22G40950.08
31A41100.08
32J41100.08
41A39650.11
42M39650.11
51A40030.1
52P40030.1
61B37170.1
62E37170.1
71B37490.09
72H37490.09
81B38200.09
82K38200.09
91B37850.09
92N37850.09
101B37580.1
102Q37580.1
111C59300.1
112F59300.1
121C59510.09
122I59510.09
131C61110.06
132L61110.06
141C59820.09
142O59820.09
151C59660.09
152R59660.09
161D41610.07
162G41610.07
171D40570.09
172J40570.09
181D39830.11
182M39830.11
191D40010.11
192P40010.11
201E38370.08
202H38370.08
211E36940.11
212K36940.11
221E37210.1
222N37210.1
231E37260.11
232Q37260.11
241F60690.07
242I60690.07
251F59130.09
252L59130.09
261F59040.1
262O59040.1
271F58930.1
272R58930.1
281G40790.08
282J40790.08
291G39690.1
292M39690.1
301G39930.1
302P39930.1
311H37280.1
312K37280.1
321H37220.11
322N37220.11
331H36960.11
332Q36960.11
341I59740.09
342L59740.09
351I59350.1
352O59350.1
361I59120.1
362R59120.1
371J39200.11
372M39200.11
381J39420.11
382P39420.11
391K37940.1
392N37940.1
401K37690.1
402Q37690.1
411L59780.08
412O59780.08
421L59610.09
422R59610.09
431M40510.09
432P40510.09
441N38800.07
442Q38800.07
451O61520.06
452R61520.06
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 315 -
Rwork0.31 6580 -
all-6895 -
obs--100 %

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