[English] 日本語
Yorodumi
- PDB-6di8: Crystal structure of bovine alpha-chymotrypsin in space group P65 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6di8
TitleCrystal structure of bovine alpha-chymotrypsin in space group P65
Components
  • Chymotrypsin A chain A
  • Chymotrypsin A chain B
  • Chymotrypsin A chain C
KeywordsHYDROLASE / Trypsin-like serine protease / endopeptidase
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...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 family, serine active site. / Serine proteases, trypsin domain profile. / 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.859 Å
AuthorsMarshall, A.C. / Keiller, B.G. / Bruning, J.B.
CitationJournal: Crystals / Year: 2018
Title: Crystal Structure of Bovine Alpha-Chymotrypsin in Space Group P65
Authors: Marshall, A.C. / Keiller, B.G. / Pederick, J.L. / Abell, A.D. / Bruning, J.B.
History
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chymotrypsin A chain A
B: Chymotrypsin A chain B
C: Chymotrypsin A chain C
D: Chymotrypsin A chain A
E: Chymotrypsin A chain B
F: Chymotrypsin A chain C
G: Chymotrypsin A chain A
H: Chymotrypsin A chain B
I: Chymotrypsin A chain C
J: Chymotrypsin A chain A
K: Chymotrypsin A chain B
L: Chymotrypsin A chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,29925
Polymers101,05012
Non-polymers1,24913
Water19,8171100
1
A: Chymotrypsin A chain A
B: Chymotrypsin A chain B
C: Chymotrypsin A chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7438
Polymers25,2633
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-97 kcal/mol
Surface area10210 Å2
MethodPISA
2
D: Chymotrypsin A chain A
E: Chymotrypsin A chain B
F: Chymotrypsin A chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4555
Polymers25,2633
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-81 kcal/mol
Surface area10380 Å2
MethodPISA
3
G: Chymotrypsin A chain A
H: Chymotrypsin A chain B
I: Chymotrypsin A chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4555
Polymers25,2633
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-87 kcal/mol
Surface area10050 Å2
MethodPISA
4
J: Chymotrypsin A chain A
K: Chymotrypsin A chain B
L: Chymotrypsin A chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6477
Polymers25,2633
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-101 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.810, 126.810, 122.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain D and (resid 1 through 10 or (resid 11...
31(chain G and (resid 1 through 10 or (resid 11...
41(chain J and (resid 1 through 10 or (resid 11...
12(chain B and (resid 16 through 17 or resid 19...
22(chain E and (resid 16 through 17 or resid 19...
32(chain H and (resid 16 through 17 or resid 19...
42(chain K and (resid 16 through 17 or resid 19...
13(chain C and (resid 149 through 152 or resid 154...
23(chain F and (resid 149 through 152 or resid 154...
33(chain I and (resid 149 through 152 or resid 154...
43(chain L and (resid 149 through 152 or resid 154...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 13
211(chain D and (resid 1 through 10 or (resid 11...D1 - 10
221(chain D and (resid 1 through 10 or (resid 11...D11
231(chain D and (resid 1 through 10 or (resid 11...D1 - 13
241(chain D and (resid 1 through 10 or (resid 11...D1 - 13
251(chain D and (resid 1 through 10 or (resid 11...D1 - 13
261(chain D and (resid 1 through 10 or (resid 11...D1 - 13
311(chain G and (resid 1 through 10 or (resid 11...G1 - 10
321(chain G and (resid 1 through 10 or (resid 11...G11
331(chain G and (resid 1 through 10 or (resid 11...G1 - 13
341(chain G and (resid 1 through 10 or (resid 11...G1 - 13
351(chain G and (resid 1 through 10 or (resid 11...G1 - 13
411(chain J and (resid 1 through 10 or (resid 11...J1 - 10
421(chain J and (resid 1 through 10 or (resid 11...J11
431(chain J and (resid 1 through 10 or (resid 11...J1 - 13
112(chain B and (resid 16 through 17 or resid 19...B16 - 17
122(chain B and (resid 16 through 17 or resid 19...B19 - 48
132(chain B and (resid 16 through 17 or resid 19...B50 - 62
142(chain B and (resid 16 through 17 or resid 19...B64
152(chain B and (resid 16 through 17 or resid 19...B0
162(chain B and (resid 16 through 17 or resid 19...B72 - 75
172(chain B and (resid 16 through 17 or resid 19...B79 - 89
182(chain B and (resid 16 through 17 or resid 19...B0
192(chain B and (resid 16 through 17 or resid 19...B16 - 146
1102(chain B and (resid 16 through 17 or resid 19...B16 - 146
1112(chain B and (resid 16 through 17 or resid 19...B16 - 146
212(chain E and (resid 16 through 17 or resid 19...E16 - 17
222(chain E and (resid 16 through 17 or resid 19...E19 - 35
232(chain E and (resid 16 through 17 or resid 19...E36
242(chain E and (resid 16 through 17 or resid 19...E16 - 146
252(chain E and (resid 16 through 17 or resid 19...E16 - 146
262(chain E and (resid 16 through 17 or resid 19...E16 - 146
272(chain E and (resid 16 through 17 or resid 19...E16 - 146
312(chain H and (resid 16 through 17 or resid 19...H16 - 17
322(chain H and (resid 16 through 17 or resid 19...H19 - 48
332(chain H and (resid 16 through 17 or resid 19...H50 - 62
342(chain H and (resid 16 through 17 or resid 19...H64
352(chain H and (resid 16 through 17 or resid 19...H77 - 8
362(chain H and (resid 16 through 17 or resid 19...H77 - 90
372(chain H and (resid 16 through 17 or resid 19...H16 - 146
382(chain H and (resid 16 through 17 or resid 19...H16 - 146
392(chain H and (resid 16 through 17 or resid 19...H16 - 146
3102(chain H and (resid 16 through 17 or resid 19...H16 - 146
3112(chain H and (resid 16 through 17 or resid 19...H16 - 146
3122(chain H and (resid 16 through 17 or resid 19...H16 - 146
3132(chain H and (resid 16 through 17 or resid 19...H16 - 146
412(chain K and (resid 16 through 17 or resid 19...K16 - 17
422(chain K and (resid 16 through 17 or resid 19...K19 - 35
432(chain K and (resid 16 through 17 or resid 19...K36
442(chain K and (resid 16 through 17 or resid 19...K16 - 146
452(chain K and (resid 16 through 17 or resid 19...K16 - 146
462(chain K and (resid 16 through 17 or resid 19...K16 - 146
113(chain C and (resid 149 through 152 or resid 154...C149 - 152
123(chain C and (resid 149 through 152 or resid 154...C154 - 166
133(chain C and (resid 149 through 152 or resid 154...C168 - 174
143(chain C and (resid 149 through 152 or resid 154...C149 - 245
153(chain C and (resid 149 through 152 or resid 154...C149 - 245
163(chain C and (resid 149 through 152 or resid 154...C149 - 245
173(chain C and (resid 149 through 152 or resid 154...C149 - 245
183(chain C and (resid 149 through 152 or resid 154...C149 - 245
193(chain C and (resid 149 through 152 or resid 154...C149 - 245
1103(chain C and (resid 149 through 152 or resid 154...C149 - 245
213(chain F and (resid 149 through 152 or resid 154...F149 - 152
223(chain F and (resid 149 through 152 or resid 154...F154 - 166
233(chain F and (resid 149 through 152 or resid 154...F168 - 174
243(chain F and (resid 149 through 152 or resid 154...F175
253(chain F and (resid 149 through 152 or resid 154...F149 - 245
263(chain F and (resid 149 through 152 or resid 154...F149 - 245
273(chain F and (resid 149 through 152 or resid 154...F149 - 245
283(chain F and (resid 149 through 152 or resid 154...F149 - 245
293(chain F and (resid 149 through 152 or resid 154...F149 - 245
2103(chain F and (resid 149 through 152 or resid 154...F149 - 245
313(chain I and (resid 149 through 152 or resid 154...I149 - 152
323(chain I and (resid 149 through 152 or resid 154...I154 - 166
333(chain I and (resid 149 through 152 or resid 154...I168 - 174
343(chain I and (resid 149 through 152 or resid 154...I175
353(chain I and (resid 149 through 152 or resid 154...I149 - 245
363(chain I and (resid 149 through 152 or resid 154...I149 - 245
373(chain I and (resid 149 through 152 or resid 154...I149 - 245
383(chain I and (resid 149 through 152 or resid 154...I149 - 245
393(chain I and (resid 149 through 152 or resid 154...I149 - 245
3103(chain I and (resid 149 through 152 or resid 154...I149 - 245
413(chain L and (resid 149 through 152 or resid 154...L149 - 152
423(chain L and (resid 149 through 152 or resid 154...L154 - 166
433(chain L and (resid 149 through 152 or resid 154...L168 - 191
443(chain L and (resid 149 through 152 or resid 154...L193 - 245

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein/peptide
Chymotrypsin A chain A


Mass: 1253.511 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / References: UniProt: P00766, chymotrypsin
#2: Protein
Chymotrypsin A chain B


Mass: 13934.556 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / References: UniProt: P00766, chymotrypsin
#3: Protein
Chymotrypsin A chain C


Mass: 10074.495 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / References: UniProt: P00766, chymotrypsin
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1100 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Protein (lyophilized powder, Worthington, code: CDTLCK) was dissolved in 0.1 M HEPES (pH 7.0) to a final concentration of 20mg/mL. Crystallisation condition was 2 M ammonium sulphate, with ...Details: Protein (lyophilized powder, Worthington, code: CDTLCK) was dissolved in 0.1 M HEPES (pH 7.0) to a final concentration of 20mg/mL. Crystallisation condition was 2 M ammonium sulphate, with equal volume (1 uL) of protein and reservoir solution in the drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.86→29.55 Å / Num. obs: 93385 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 25.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.041 / Rrim(I) all: 0.126 / Net I/σ(I): 12.2 / Num. measured all: 868057 / Scaling rejects: 1475
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.86-1.896.81.9243130846060.3830.7792.083199.7
10.18-29.559.50.04255235790.9990.0140.04529.396.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.67 Å29.55 Å
Translation3.67 Å29.55 Å

-
Processing

Software
NameVersionClassificationNB
PHENIX(dev_3084)refinement
MOSFLMdata reduction
Aimless0.5.17data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q2K

4q2k


Resolution: 1.859→28.132 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 4889 5.25 %
Rwork0.1885 88296 -
obs0.1904 93185 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.53 Å2 / Biso mean: 34.8988 Å2 / Biso min: 5.08 Å2
Refinement stepCycle: final / Resolution: 1.859→28.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7049 0 65 1100 8214
Biso mean--82.63 44.01 -
Num. residues----964
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A209X-RAY DIFFRACTION5.355TORSIONAL
12D209X-RAY DIFFRACTION5.355TORSIONAL
13G209X-RAY DIFFRACTION5.355TORSIONAL
14J209X-RAY DIFFRACTION5.355TORSIONAL
21B2082X-RAY DIFFRACTION5.355TORSIONAL
22E2082X-RAY DIFFRACTION5.355TORSIONAL
23H2082X-RAY DIFFRACTION5.355TORSIONAL
24K2082X-RAY DIFFRACTION5.355TORSIONAL
31C1659X-RAY DIFFRACTION5.355TORSIONAL
32F1659X-RAY DIFFRACTION5.355TORSIONAL
33I1659X-RAY DIFFRACTION5.355TORSIONAL
34L1659X-RAY DIFFRACTION5.355TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.859-1.88010.35411620.33662900306299
1.8801-1.90230.33871390.32782951309099
1.9023-1.92550.33421670.331129363103100
1.9255-1.94980.36241700.310129563126100
1.9498-1.97550.36331740.288229163090100
1.9755-2.00250.32821780.27729183096100
2.0025-2.03110.32761710.263129003071100
2.0311-2.06140.31161770.247329333110100
2.0614-2.09360.28651600.251529593119100
2.0936-2.1280.28271340.24329633097100
2.128-2.16460.25161180.239530013119100
2.1646-2.2040.23421720.23129293101100
2.204-2.24640.26371860.227229063092100
2.2464-2.29220.2621600.217529503110100
2.2922-2.3420.22631950.201329353130100
2.342-2.39650.2641590.201229383097100
2.3965-2.45640.27331510.200129273078100
2.4564-2.52270.23091640.197129533117100
2.5227-2.59690.26391740.183229353109100
2.5969-2.68070.21371430.184229403083100
2.6807-2.77640.25831790.187629513130100
2.7764-2.88750.23481460.196429863132100
2.8875-3.01870.23511760.196829163092100
3.0187-3.17770.21681430.17729753118100
3.1777-3.37650.19211710.170129393110100
3.3765-3.63670.18671740.14729473121100
3.6367-4.00170.1761490.134429893138100
4.0017-4.57860.14941600.12229573117100
4.5786-5.76040.16831590.144929843143100
5.7604-28.1350.2081780.18672906308497
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0793-0.73820.70093.9764-3.44787.27150.107-0.27480.31770.48070.1968-0.38560.18310.8093-0.21520.32440.0809-0.03910.2483-0.09390.2056-57.9569-3.56116.9562
23.5427-1.49550.35423.84960.821.8956-0.0131-0.1732-0.14770.01580.0772-0.16050.24990.0582-0.05210.22040.0364-0.00430.14120.01780.1469-53.2852-15.3899-0.2665
33.86451.2427-0.57841.8490.75974.12650.0930.38320.0375-0.4946-0.0443-0.0825-0.003-0.0751-0.04350.32470.0656-0.00060.17050.00760.1542-53.4071-17.2526-11.98
48.93998.9901-3.8692.0119-1.28545.71490.3551-0.4949-1.53760.5466-0.0732-0.83130.57-0.7144-0.29770.40830.0047-0.1160.41960.05840.4128-62.3928-19.83034.071
56.07521.17730.62321.905-0.48121.87160.01250.6192-0.3793-0.6881-0.1185-0.68960.22220.33020.10540.47630.13280.18240.27020.01460.3855-45.9927-14.6202-15.4248
61.5016-0.3088-0.10142.8089-0.61561.7904-0.02140.12810.0433-0.1346-0.0215-0.4009-0.07310.12280.03240.22910.03090.01580.1214-0.01750.1966-51.8851-8.4341-3.1528
71.9985-8.15558.81988.6113-3.75566.762-0.0951-1.7837-0.5823-0.04010.8531.1798-0.5613-0.5934-0.69690.41370.1659-0.10780.32960.02750.4418-48.9871-23.18749.264
83.25860.4619-0.08015.943-2.05962.7216-0.1678-0.65230.44850.1036-0.0928-0.5589-0.09150.32170.2250.24650.0617-0.08910.1911-0.08840.2837-46.0684-7.26055.8171
94.4154-0.8368-1.82362.3589-0.5683.0083-0.0513-0.20950.51960.0492-0.1967-1.5338-0.05911.31760.27010.30980.02210.01910.4550.10730.9127-31.4035-4.5871-4.0381
102.73690.37691.5934.8378-0.4444.4343-0.0712-0.06960.1945-0.03870.0279-0.47260.00620.18590.04150.1840.03330.02520.1629-0.02230.2403-45.8003-7.284-0.5712
111.9738-0.92071.24814.1873-2.43214.01930.07320.12050.10490.0061-0.1992-0.94580.23540.52040.1430.21740.06150.00660.2204-0.01550.4361-37.7799-8.9228-1.4026
125.47910.40812.32028.45510.49656.2784-0.28090.3042-0.2086-1.15490.2733-0.57460.4506-0.30.00540.59480.02240.06780.24140.0230.2268-51.5501-4.5947-20.2999
131.869-0.9453-2.06860.64390.22976.4788-0.1285-0.029-0.39630.1456-0.12410.2954-0.0359-0.27780.30670.26050.013-0.0390.1525-0.0040.4728-69.16955.35647.9602
141.7392-0.19440.52721.8539-1.34952.3839-0.10680.00970.02210.02150.1061-0.1723-0.3304-0.01010.00770.28170.0199-0.00290.1155-0.04050.281-73.90917.6485-4.5107
159.77767.19433.51739.4323-0.12687.37050.151-0.68780.61961.1813-0.54470.2639-1.28010.11820.40980.5946-0.0403-0.02910.3004-0.02660.4291-64.435521.50373.9774
167.2661.45471.12182.50470.28212.9608-0.05980.21290.0529-0.62970.05660.3345-0.3539-0.20770.00850.39710.0575-0.05760.1377-0.03530.2565-80.898216.26-15.2859
171.193-0.05480.25222.9478-0.0361.583-0.01870.0208-0.28580.00750.1065-0.04830.0391-0.0435-0.09020.22320.0267-0.01350.1163-0.0230.3532-74.62359.559-3.9156
181.99841.9975-8.30899.9095.55282.00710.3345-0.30570.73010.34490.5748-1.06270.42590.0806-0.93090.5920.13060.00650.29860.02440.4296-78.275824.71669.3868
192.1167-0.3460.04083.0585-0.33351.9729-0.0146-0.1785-0.2560.4087-0.01610.1950.1854-0.10860.01280.26820.06370.08960.1590.03750.3794-80.79678.55035.7363
202.9938-0.21133.4269.41490.29866.15480.2977-0.3204-1.410.4467-0.29181.5830.0692-0.98150.00190.31890.00510.03950.4015-0.02231.106-98.02645.3018-2.1313
211.77950.1819-0.59623.4224-0.13843.8743-0.01-0.0416-0.53910.1391-0.02790.4045-0.0364-0.30180.03060.2150.04150.00180.15860.03430.4523-84.49898.077-1.1879
221.11830.0968-0.96331.8562-0.30123.52490.03170.1937-0.3319-0.1231-0.06520.3586-0.0446-0.33460.04840.22440.012-0.05530.1464-0.0350.4076-82.88528.1677-7.7496
236.61114.6759-0.3758.85912.9393.2783-0.18760.5630.6074-0.27330.21380.64350.2048-0.52730.02560.2128-0.0519-0.01190.22580.07480.2357-69.585-3.258513.2664
247.01234.2888-0.75414.3816-0.33560.0649-0.4520.86450.1419-0.41830.41580.3165-0.17490.0204-0.01420.2553-0.0551-0.04090.210.06260.1867-73.7038-10.556612.7156
254.32411.0014-1.02586.9759-3.87995.11140.00050.1287-0.66890.01210.00610.41880.6097-0.2099-0.0240.3643-0.0643-0.04020.2375-0.03220.3337-73.1481-23.30224.9804
265.82371.3458-0.15274.7362-0.5833.70750.1747-0.2865-0.06170.2137-0.06260.20040.195-0.2456-0.11030.3107-0.0534-0.00050.15680.01620.1018-73.639-14.64326.7646
273.9379-1.22580.31822.15780.09673.82360.1725-0.4939-0.02790.6062-0.04120.1511-0.16970.1233-0.09640.3467-0.06920.01110.1916-0.0040.144-73.5189-16.883331.7019
289.2216-8.9534-5.09472.01311.81396.39190.22070.6178-1.3724-0.9665-0.29951.06770.23260.33390.00330.4040.0015-0.10920.3991-0.06370.4019-64.3776-19.833115.6177
292.0584-3.2108-4.55373.53461.61819.1959-0.0528-0.2833-0.59070.5394-0.04590.37580.20890.30250.02070.4288-0.0928-0.00710.2950.00480.1885-70.3274-17.999934.8941
305.52610.0652-0.90112.36370.00852.63560.0793-0.7403-0.11010.853-0.15810.61170.3114-0.25210.08780.4771-0.11960.19490.2798-0.0430.3344-80.3349-12.955434.928
312.0997-0.4875-0.18013.62170.31751.5887-0.0032-0.23680.25310.09970.00120.3224-0.2859-0.05380.02020.3388-0.0473-0.00410.1758-0.02360.224-73.2156-0.868325.0324
325.63251.10140.34636.4340.94730.5812-0.0903-0.0686-0.5432-0.54220.17810.388-0.0012-0.2534-0.08040.2459-0.0536-0.06120.19460.05450.213-80.6573-13.286814.4779
334.00353.39850.31814.73870.76041.98020.03650.24990.0591-0.23820.01690.0432-0.0136-0.1557-0.0510.2298-0.0588-0.07490.22270.05840.1819-79.8524-12.044512.9936
345.43230.8373-4.39935.6420.31076.89830.23010.69221.203-0.20490.15881.342-0.0931-1.267-0.40670.3005-0.0461-0.01080.5803-0.06361.0622-98.0632-4.764322.0193
354.692.45541.78454.6774-3.32317.8008-0.2066-0.27590.20440.289-0.29281.2874-0.2439-1.17110.5050.2694-0.01340.08120.2865-0.10260.6605-91.4624-4.394726.2523
363.3444-1.04261.48374.6729-0.12554.756-0.01570.00590.1970.11080.00630.49450.0535-0.16140.00030.1813-0.02910.03910.15910.01580.2311-80.9648-7.09120.3064
372.1555-0.45951.48357.00410.16594.79540.067-0.01820.48710.4396-0.53830.791-0.2428-0.10870.43850.3219-0.0827-0.14450.3062-0.0130.7078-92.6886-14.222414.1461
383.89670.77132.25074.36761.31634.4142-0.0704-0.37540.38320.8756-0.24320.50810.3041-0.27550.34970.403-0.06330.14480.191-0.0440.2936-80.1513-4.616934.0237
391.49730.6569-1.97570.88930.26324.9204-0.01430.0773-0.3889-0.39270.0954-0.0610.25590.1793-0.05340.28-0.0048-0.01180.1643-0.05690.4524-57.61865.358611.7021
402.49280.074-0.4172.85160.86281.8429-0.05810.2162-0.3085-0.39590.09250.214-0.13480.0284-0.0650.2545-0.0439-0.03120.1505-0.01780.3288-52.970712.04312.7086
416.16011.55821.3857.7153.4085.6172-0.27-0.00770.9918-0.63140.1140.408-0.91050.19740.16770.3089-0.0461-0.0010.19230.03470.3531-52.936625.229325.0944
427.17451.8247-0.09122.84191.07523.6274-0.390.3778-0.2698-0.16840.32910.0702-0.2224-0.0795-0.01040.2959-0.0069-0.05140.11520.01710.2754-52.835316.26726.706
433.3321-0.24620.86780.3410.56872.53970.0603-0.2145-0.04780.3096-0.00220.3095-0.1871-0.0808-0.03840.3353-0.01020.02140.14180.04040.3-53.381418.234831.6083
442.0004-8.415-1.15559.29432.85152.0210.3280.52140.7071-0.7696-0.51170.1198-1.9182-0.3310.1360.5169-0.0013-0.08020.33910.040.4129-62.060921.171515.5098
452.0474-2.36786.68015.5717-0.03026.0702-0.0753-0.02980.11210.42450.10770.1477-0.5612-0.1129-0.07170.3960.00850.08610.27910.09590.3226-56.222120.094534.7791
462.01661.5119-2.01212.73122.16534.7842-0.1413-0.4878-0.00360.7826-0.2245-0.9602-0.35860.51120.24050.3778-0.0422-0.18240.24370.07270.4815-37.750213.270335.2589
471.99882.10281.74224.26310.51253.9305-0.1612-0.37530.21540.4866-0.10270.5553-0.3264-0.40040.22780.33420.02360.04480.17150.02860.3683-58.926516.297334.3325
480.63730.3826-0.35553.758-0.41351.70140.0199-0.1513-0.58240.06940.1363-0.09750.21080.0246-0.15120.2807-0.0337-0.04690.12450.02350.4647-53.68522.46725.1724
493.93640.62340.76594.2824-0.72212.3555-0.03370.14690.0813-0.4891-0.001-0.2298-0.16140.25150.04020.2851-0.06260.02880.1725-0.060.2842-45.876614.609214.4912
503.4771.8151-0.76335.3341-0.76023.7266-0.190.52150.1918-0.23220.3345-0.4684-0.4549-0.0405-0.12130.3515-0.07020.0030.178-0.03110.3082-51.004319.756410.9435
511.94942.12541.67412.88751.98272.69-0.08070.4539-1.0336-0.31410.3423-1.45330.04030.9962-0.16660.313-0.00460.05720.3918-0.02490.8678-32.17914.430620.2251
522.1802-0.11020.00242.89571.03333.5090.01440.0117-0.5293-0.1598-0.0519-0.33780.01170.21350.01860.2253-0.0370.01360.1504-0.03330.4562-42.34958.08820.9668
531.1464-0.1362-0.77931.54170.12422.83950.0879-0.1693-0.28850.1111-0.0172-0.2445-0.07280.2523-0.06530.2304-0.0177-0.04710.13880.02990.3792-43.92058.167827.4651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A1 - 13
2X-RAY DIFFRACTION2chain 'B' and (resid 16 through 48 )B16 - 48
3X-RAY DIFFRACTION3chain 'B' and (resid 49 through 68 )B49 - 68
4X-RAY DIFFRACTION4chain 'B' and (resid 69 through 80 )B69 - 80
5X-RAY DIFFRACTION5chain 'B' and (resid 81 through 103 )B81 - 103
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 146 )B104 - 146
7X-RAY DIFFRACTION7chain 'C' and (resid 149 through 153 )C149 - 153
8X-RAY DIFFRACTION8chain 'C' and (resid 154 through 164 )C154 - 164
9X-RAY DIFFRACTION9chain 'C' and (resid 165 through 184 )C165 - 184
10X-RAY DIFFRACTION10chain 'C' and (resid 185 through 215 )C185 - 215
11X-RAY DIFFRACTION11chain 'C' and (resid 216 through 234 )C216 - 234
12X-RAY DIFFRACTION12chain 'C' and (resid 235 through 245 )C235 - 245
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 13 )D1 - 13
14X-RAY DIFFRACTION14chain 'E' and (resid 16 through 68 )E16 - 68
15X-RAY DIFFRACTION15chain 'E' and (resid 69 through 80 )E69 - 80
16X-RAY DIFFRACTION16chain 'E' and (resid 81 through 103 )E81 - 103
17X-RAY DIFFRACTION17chain 'E' and (resid 104 through 146 )E104 - 146
18X-RAY DIFFRACTION18chain 'F' and (resid 149 through 153 )F149 - 153
19X-RAY DIFFRACTION19chain 'F' and (resid 154 through 164 )F154 - 164
20X-RAY DIFFRACTION20chain 'F' and (resid 165 through 175 )F165 - 175
21X-RAY DIFFRACTION21chain 'F' and (resid 176 through 205 )F176 - 205
22X-RAY DIFFRACTION22chain 'F' and (resid 206 through 245 )F206 - 245
23X-RAY DIFFRACTION23chain 'G' and (resid 1 through 13 )G1 - 13
24X-RAY DIFFRACTION24chain 'H' and (resid 16 through 29 )H16 - 29
25X-RAY DIFFRACTION25chain 'H' and (resid 30 through 39 )H30 - 39
26X-RAY DIFFRACTION26chain 'H' and (resid 40 through 48 )H40 - 48
27X-RAY DIFFRACTION27chain 'H' and (resid 49 through 68 )H49 - 68
28X-RAY DIFFRACTION28chain 'H' and (resid 69 through 80 )H69 - 80
29X-RAY DIFFRACTION29chain 'H' and (resid 81 through 90 )H81 - 90
30X-RAY DIFFRACTION30chain 'H' and (resid 91 through 113 )H91 - 113
31X-RAY DIFFRACTION31chain 'H' and (resid 114 through 133 )H114 - 133
32X-RAY DIFFRACTION32chain 'H' and (resid 134 through 146 )H134 - 146
33X-RAY DIFFRACTION33chain 'I' and (resid 149 through 164 )I149 - 164
34X-RAY DIFFRACTION34chain 'I' and (resid 165 through 175 )I165 - 175
35X-RAY DIFFRACTION35chain 'I' and (resid 176 through 184 )I176 - 184
36X-RAY DIFFRACTION36chain 'I' and (resid 185 through 215 )I185 - 215
37X-RAY DIFFRACTION37chain 'I' and (resid 216 through 224 )I216 - 224
38X-RAY DIFFRACTION38chain 'I' and (resid 225 through 245 )I225 - 245
39X-RAY DIFFRACTION39chain 'J' and (resid 1 through 13 )J1 - 13
40X-RAY DIFFRACTION40chain 'K' and (resid 16 through 29 )K16 - 29
41X-RAY DIFFRACTION41chain 'K' and (resid 30 through 39 )K30 - 39
42X-RAY DIFFRACTION42chain 'K' and (resid 40 through 48 )K40 - 48
43X-RAY DIFFRACTION43chain 'K' and (resid 49 through 68 )K49 - 68
44X-RAY DIFFRACTION44chain 'K' and (resid 69 through 80 )K69 - 80
45X-RAY DIFFRACTION45chain 'K' and (resid 81 through 90 )K81 - 90
46X-RAY DIFFRACTION46chain 'K' and (resid 91 through 103 )K91 - 103
47X-RAY DIFFRACTION47chain 'K' and (resid 104 through 113 )K104 - 113
48X-RAY DIFFRACTION48chain 'K' and (resid 114 through 133 )K114 - 133
49X-RAY DIFFRACTION49chain 'K' and (resid 134 through 146 )K134 - 146
50X-RAY DIFFRACTION50chain 'L' and (resid 149 through 158 )L149 - 158
51X-RAY DIFFRACTION51chain 'L' and (resid 159 through 175 )L159 - 175
52X-RAY DIFFRACTION52chain 'L' and (resid 176 through 205 )L176 - 205
53X-RAY DIFFRACTION53chain 'L' and (resid 206 through 245 )L206 - 245

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more