[English] 日本語
Yorodumi
- PDB-6x3m: Crystal structure of full-length Streptococcal bacteriophage hyal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x3m
TitleCrystal structure of full-length Streptococcal bacteriophage hyaluronidase in complex with unsaturated hyaluronan octa-saccharides
ComponentsHyaluronoglucosaminidase
KeywordsLYASE / HylP / Hyaluronidase / S. pyogenes phage H4489A / Beta-elimination / unsaturated Hyaluronan Octa-saccharides
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / hyaluronoglucosaminidase / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / symbiont entry into host cell via disruption of host cell envelope / virion component
Similarity search - Function
Hyaluronidase, bacterial / Hyaluronidase protein (HylP) / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain
Similarity search - Domain/homology
Hyaluronoglucosaminidase
Similarity search - Component
Biological speciesStreptococcus pyogenes phage H4489A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.581 Å
AuthorsDeivanayagam, C. / Schormann, N.
CitationJournal: To Be Published
Title: Crystal Structure of Streptococcal Bacteriophage Hyaluronidase: Presence of a Prokaryotic Collagen and Elucidation of Catalytic Mechanism
Authors: Lee, J.H. / Schormann, N. / Rajashankar, K.R. / Deivanaygam, C.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hyaluronoglucosaminidase
B: Hyaluronoglucosaminidase
C: Hyaluronoglucosaminidase
D: Hyaluronoglucosaminidase
E: Hyaluronoglucosaminidase
F: Hyaluronoglucosaminidase
G: Hyaluronoglucosaminidase
H: Hyaluronoglucosaminidase
I: Hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,28527
Polymers365,8029
Non-polymers20,48318
Water00
1
A: Hyaluronoglucosaminidase
B: Hyaluronoglucosaminidase
C: Hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7629
Polymers121,9343
Non-polymers6,8286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75080 Å2
ΔGint-175 kcal/mol
Surface area45780 Å2
MethodPISA
2
D: Hyaluronoglucosaminidase
E: Hyaluronoglucosaminidase
F: Hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7629
Polymers121,9343
Non-polymers6,8286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74740 Å2
ΔGint-170 kcal/mol
Surface area46110 Å2
MethodPISA
3
G: Hyaluronoglucosaminidase
H: Hyaluronoglucosaminidase
I: Hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7629
Polymers121,9343
Non-polymers6,8286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75950 Å2
ΔGint-160 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)338.168, 56.797, 276.954
Angle α, β, γ (deg.)90.000, 126.680, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 234 or resid 236...
21(chain B and (resid 8 through 234 or resid 236...
31(chain C and (resid 8 through 234 or resid 236...
41(chain D and (resid 8 through 234 or resid 236 through 346 or resid 348 through 356))
51(chain E and (resid 8 through 234 or resid 236 through 351 or resid 353 through 356))
61(chain F and (resid 8 through 234 or resid 236...
71(chain G and (resid 8 through 234 or resid 236...
81(chain H and (resid 8 through 346 or resid 348 through 351 or resid 353 through 356))
91(chain I and (resid 8 through 234 or resid 236...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEU(chain A and (resid 8 through 234 or resid 236...AA8 - 2348 - 234
12ILEILETHRTHR(chain A and (resid 8 through 234 or resid 236...AA236 - 346236 - 346
13GLYGLYGLYGLY(chain A and (resid 8 through 234 or resid 236...AA348348
21ARGARGLEULEU(chain B and (resid 8 through 234 or resid 236...BB8 - 2348 - 234
22ILEILETHRTHR(chain B and (resid 8 through 234 or resid 236...BB236 - 346236 - 346
23PROPROLEULEU(chain B and (resid 8 through 234 or resid 236...BB6 - 3676 - 367
31ARGARGLEULEU(chain C and (resid 8 through 234 or resid 236...CC8 - 2348 - 234
32ILEILETHRTHR(chain C and (resid 8 through 234 or resid 236...CC236 - 346236 - 346
33GLYGLYGLYGLY(chain C and (resid 8 through 234 or resid 236...CC348348
41ARGARGLEULEU(chain D and (resid 8 through 234 or resid 236 through 346 or resid 348 through 356))DD8 - 2348 - 234
42ILEILETHRTHR(chain D and (resid 8 through 234 or resid 236 through 346 or resid 348 through 356))DD236 - 346236 - 346
43GLYGLYTYRTYR(chain D and (resid 8 through 234 or resid 236 through 346 or resid 348 through 356))DD348 - 356348 - 356
51ARGARGLEULEU(chain E and (resid 8 through 234 or resid 236 through 351 or resid 353 through 356))EE8 - 2348 - 234
52ILEILEALAALA(chain E and (resid 8 through 234 or resid 236 through 351 or resid 353 through 356))EE236 - 351236 - 351
53THRTHRTYRTYR(chain E and (resid 8 through 234 or resid 236 through 351 or resid 353 through 356))EE353 - 356353 - 356
61ARGARGLEULEU(chain F and (resid 8 through 234 or resid 236...FF8 - 2348 - 234
62ILEILETHRTHR(chain F and (resid 8 through 234 or resid 236...FF236 - 346236 - 346
63GLYGLYALAALA(chain F and (resid 8 through 234 or resid 236...FF348 - 351348 - 351
64THRTHRTYRTYR(chain F and (resid 8 through 234 or resid 236...FF353 - 356353 - 356
71ARGARGLEULEU(chain G and (resid 8 through 234 or resid 236...GG8 - 2348 - 234
72ILEILETHRTHR(chain G and (resid 8 through 234 or resid 236...GG236 - 346236 - 346
73GLYGLYGLYGLY(chain G and (resid 8 through 234 or resid 236...GG348348
81ARGARGTHRTHR(chain H and (resid 8 through 346 or resid 348 through 351 or resid 353 through 356))HH8 - 3468 - 346
82GLYGLYALAALA(chain H and (resid 8 through 346 or resid 348 through 351 or resid 353 through 356))HH348 - 351348 - 351
83THRTHRTYRTYR(chain H and (resid 8 through 346 or resid 348 through 351 or resid 353 through 356))HH353 - 356353 - 356
91ARGARGLEULEU(chain I and (resid 8 through 234 or resid 236...II8 - 2348 - 234
92ILEILETHRTHR(chain I and (resid 8 through 234 or resid 236...II236 - 346236 - 346
93PROPROLEULEU(chain I and (resid 8 through 234 or resid 236...II6 - 3676 - 367

-
Components

#1: Protein
Hyaluronoglucosaminidase / Hyaluronidase


Mass: 40644.656 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes phage H4489A (virus)
Gene: HYLP1, HYLP / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15316, hyaluronate lyase
#2: Polysaccharide
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 758.633 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-3/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-4-deoxy-GlcpA]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1517.267 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-2-1-2-1-3/a3-b1_b4-c1_c3-d1_d4-e1_e3-f1_f4-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-4-deoxy-IdopA]{}}}}}}}}LINUCSPDB-CARE
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17.5-18.5% (w/v) PEG 2000 MME, 70 mM KBr, 62.5 mM Glycine, 100 mM Tris-HCl, pH 8.5; prior to crystallization the protein was incubated with unsaturated hyaluronan octa-saccharides at a molar ratio of 1:50

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.581→35 Å / Num. obs: 49298 / % possible obs: 97.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 91.96 Å2 / Rmerge(I) obs: 0.124 / Χ2: 1.537 / Net I/av σ(I): 14.4 / Net I/σ(I): 6.5
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 4295 / Χ2: 1.068 / % possible all: 86.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C3F, 1BKV

2c3f

1bkv


Resolution: 3.581→29.867 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2991 2519 5.17 %
Rwork0.2473 46186 -
obs0.25 48705 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.47 Å2 / Biso mean: 105.6094 Å2 / Biso min: 28.32 Å2
Refinement stepCycle: final / Resolution: 3.581→29.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24172 0 1402 0 25574
Biso mean--96.31 --
Num. residues----3241
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9315X-RAY DIFFRACTION9.214TORSIONAL
12B9315X-RAY DIFFRACTION9.214TORSIONAL
13C9315X-RAY DIFFRACTION9.214TORSIONAL
14D9315X-RAY DIFFRACTION9.214TORSIONAL
15E9315X-RAY DIFFRACTION9.214TORSIONAL
16F9315X-RAY DIFFRACTION9.214TORSIONAL
17G9315X-RAY DIFFRACTION9.214TORSIONAL
18H9315X-RAY DIFFRACTION9.214TORSIONAL
19I9315X-RAY DIFFRACTION9.214TORSIONAL
LS refinement shellResolution: 3.581→3.6498 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.354 113 -
Rwork0.3234 1907 -
obs--73 %
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)
15.0295-2.7895-0.38163.9134-1.97467.5788-0.0135-0.2486-1.7-0.24940.46140.82960.9545-1.1019-0.35111.0866-0.1954-0.03330.4360.13630.8549-16.1249-40.1061111.352
23.2092-0.1436-0.40325.1518-5.32097.1834-0.1498-0.0701-0.5110.19720.21030.76430.0255-0.741-0.04070.4951-0.0779-0.07630.7501-0.06690.5576-17.7003-32.582699.5699
30.1221-0.63871.29431.3614-3.42387.3368-0.19890.08890.11380.2223-0.0745-0.0659-0.3305-0.00830.14710.6403-0.0094-0.19090.82680.10870.5342-28.5149-5.354-18.7302
45.7753-0.84072.53692.4767-3.66578.5301-0.1864-0.72390.43170.59590.0044-1.0544-1.0245-0.80860.05481.0010.0917-0.29730.63050.08310.8207-40.234827.3863-67.4063
53.6601-1.44771.65083.9511-2.30975.88430.159-0.2151-0.40130.00970.06220.51820.4785-1.6034-0.19460.5679-0.1724-0.17030.83950.03590.4587-52.610920.1544-81.6693
64.4835-1.00480.91792.7175-0.61641.20270.01890.41740.1918-0.59360.66230.1320.463-1.1596-0.44130.4527-0.0025-0.16421.46140.27240.4921-59.767934.215-102.7723
70.7603-0.0481-0.42070.09320.22510.67520.01740.78520.69330.01820-0.1113-0.1481-0.05260.01980.8517-0.0899-0.57612.23750.85221.1192-71.961154.45-130.359
80.20740.09210.69550.5219-0.3246.5182-0.0188-0.03960.39090.1055-0.17090.0712-0.7492-0.24040.18570.73740.0233-0.05090.24430.01510.5416-9.2303-24.153682.4211
90.3173-0.54951.68151.4227-3.04937.53130.2926-0.0445-0.1153-0.22780.02220.13650.6835-0.2244-0.37480.556-0.0474-0.1030.75110.22130.6628-31.55421.2695-36.2757
103.3758-0.6252.02512.0553-1.15192.6497-0.337-0.2266-0.2150.14010.64310.3506-0.1229-1.2378-0.31930.4136-0.0399-0.06971.11440.20460.4969-54.865825.846-83.119
110.4711-0.44731.21890.5833-1.08312.7513-0.19551.06870.3947-0.23160.04950.1083-0.0538-0.10650.00940.4604-0.1766-0.33461.98840.68380.8971-63.633441.7345-117.5605
120.1428-0.14670.95020.4209-1.64114.99350.3260.0738-0.0763-0.11330.20230.25170.7023-0.2004-0.40920.99560.1360.04140.3810.07080.5285-10.5549-29.05658.4272
132.2749-0.54332.21781.1309-1.98125.315-0.2130.07420.19230.09660.5230.2687-0.1069-1.3047-0.26970.4636-0.0668-0.15511.00780.24350.5183-54.814929.2025-90.8158
147.66860.23273.25363.23540.60556.64920.2755-1.21490.410.2281-0.61210.611-0.8055-0.74630.28980.7944-0.27270.2180.544-0.05840.6065-14.5809-6.0725185.9468
152.55841.0719-1.65732.4427-0.9085.4992-0.04870.66680.3304-0.3074-0.46020.2086-0.352-1.43590.4870.63550.0722-0.32180.8402-0.01230.7897-15.4445-0.0245173.3798
160.3991-0.51490.141.1085-1.61844.1957-0.098-0.01380.1752-0.1392-0.584-0.2233-0.22670.54920.77091.1352-0.0758-0.06950.7213-0.08160.5772-16.9217.738982.7555
171.34281.24161.16661.8926-1.38768.77460.1152-0.1105-0.10220.3568-0.1891-0.45261.6696-0.57660.07820.6927-0.0542-0.04010.57110.04010.566-39.448622.607220.7435
186.84681.0142.33337.10370.1644.2305-0.64110.0029-0.2655-1.0106-0.1065-0.51290.8359-0.5440.59741.0533-0.12830.18050.76450.14190.4282-45.632534.32360.1175
194.58920.56662.69843.4174-0.62863.799-0.3650.0537-0.5288-0.34250.1642-0.23681.3847-0.99770.230.951-0.33290.12040.7549-0.10710.3109-53.019136.7695-11.658
202.83790.5794-0.53142.4687-1.832.9613-0.79620.40040.3051-0.6914-0.0319-0.08930.9206-0.6422-0.08340.883-0.701-0.21561.5657-0.15910.4546-54.834541.1537-27.0065
211.26581.04710.60611.22440.14041.3942-0.0992-0.08450.0172-0.01670.10380.25840.2709-0.56680.01471.0417-0.8831-0.33651.92390.01260.4989-71.853134.06-27.8187
222.44770.44770.96831.25630.99044.2514-1.19460.71250.9094-0.77530.2830.1792-0.5673-0.06240.41420.8127-0.5655-0.52841.58760.22670.7157-60.709154.929-37.3681
232.08450.5858-0.09732.271-0.0820.7092-0.53431.24010.81140.07760.30090.0522-0.06320.36580.20951.1421-0.6074-0.38882.58580.56630.6186-73.599958.2085-55.0858
244.10851.6702-0.16896.2193.01852.35160.06770.11810.7019-0.1838-0.26051.1588-0.9847-0.25440.2150.9907-0.1207-0.07060.0818-0.05850.6179-6.755810.8155180.7367
250.535-0.20472.05320.2259-1.39497.6564-0.11430.22790.1997-0.184-0.1376-0.13440.59650.39740.15850.99660.00410.02350.88790.01550.4995-16.11219.38991.4051
262.7539-1.9937-0.62822.36320.50262.09960.0840.0902-0.4566-0.4996-0.1906-0.23180.772-0.1829-0.08860.9884-0.1706-0.07960.94690.11410.7961-40.258330.52215.7534
273.00520.57120.74272.0859-1.12674.7478-0.2884-0.32870.2268-0.00340.1124-0.11520.5653-1.15340.21560.7161-0.3953-0.10240.8409-0.01540.4288-54.125939.1465-10.1713
282.37660.50260.43240.9540.27681.0278-0.51170.82450.3542-0.64560.62120.12520.1446-0.8710.6311.2514-1.0729-0.76371.7720.05490.4498-64.919745.2287-32.5493
291.00350.43360.52080.37260.47180.8406-0.0430.1360.1434-0.24060.28890.10780.11750.23210.13761.355-1.1745-1.02482.74180.55561.0341-70.381559.021-61.6372
300.2849-0.52141.11950.2884-1.12863.31690.01160.18590.0239-0.29030.0211-0.05310.5606-0.1659-0.08771.1191-0.163-0.02320.56650.15490.5583-7.6584-0.908134.6984
311.8824-0.06421.751.5637-1.51325.2145-0.33810.20030.1216-0.45660.1837-0.29990.9238-0.98790.01240.7125-0.38150.0530.8027-0.09690.4865-52.539.6303-11.8687
320.0159-0.0146-0.0740.0020.07760.3208-0.23370.1210.226-0.73280.01880.6635-0.0989-0.12410.18841.6514-1.1951-0.71282.26770.33541.2233-75.740654.3958-63.2311
334.55220.35212.07982.50091.56128.0563-0.0192-0.7615-0.9174-0.77970.0839-0.772-0.63650.33760.090.65130.06990.13820.61180.09630.6347-154.4829-6.2611-257.5109
340.49860.0717-1.04940.6178-0.81852.7308-0.50020.1534-0.34310.0017-0.3989-0.34170.7468-0.1490.51270.6019-0.074-0.08820.52390.10210.5843-155.00061.7445-233.7191
350.98581.18431.8442.22013.07256.78690.0852-0.130.3817-0.2483-0.25280.3557-1.2948-0.04830.2291.01880.01570.15320.8644-0.03650.5383-151.370710.473-144.1314
363.5113-0.17262.86621.84761.03373.1023-0.13390.4272-0.1949-0.21370.4852-0.30450.14580.1798-0.37470.9999-0.24850.09920.6354-0.09710.4291-127.393219.3229-79.3387
374.1750.89031.20453.67030.68293.9402-0.2308-0.0670.0892-0.54120.3425-1.08050.04080.5369-0.08640.3255-0.05420.18570.5068-0.15130.6509-113.363625.016-54.214
381.9350.59542.32562.18861.54528.02550.1997-0.48680.05970.21060.122-0.47990.08540.664-0.3130.35490.0057-0.09390.7355-0.11420.6427-103.296329.9516-23.6168
390.28780.10791.60010.04110.88098.67260.0234-0.09140.08490.02410.0817-0.0033-0.50970.161-0.11020.8662-0.139-0.0230.4048-0.02070.4589-152.186911.3182-175.5574
403.14881.11743.65291.54471.26836.4575-0.00670.0096-0.1243-0.06340.1121-0.57430.01860.1886-0.10290.3736-0.03190.0130.4527-0.13440.6993-109.416627.0256-40.0731
415.41540.3989-0.28138.9558-0.35946.59110.27980.1599-0.37730.1181-0.11840.4551-0.19540.5332-0.05580.43520.01320.04270.2782-0.04510.2704-171.7075-5.2413-252.0852
420.2650.09590.87990.60651.93846.4905-0.18090.06630.3590.0874-0.194-0.0157-0.41680.2830.27171.0890.0221-0.00230.1167-0.08610.4914-161.2997-0.3658-210.4798
435.95620.3644.68493.01960.0343.68350.99490.2124-0.44150.1206-0.25860.30463.02180.2301-0.74821.1699-0.02830.12340.52440.06760.3695-148.27154.8175-135.5936
442.29620.51961.54160.23830.11612.02170.06660.37740.149-0.20610.44870.09510.46250.2905-0.45491.4937-0.19450.15060.7407-0.18860.5123-134.402220.0061-89.7876
455.5466-0.38434.22053.99152.00745.33350.42331.2383-1.1577-0.33950.6206-1.18631.08751.4299-1.08520.97390.0945-0.14471.262-0.7490.9483-114.902614.354-73.7782
464.9861.64973.41354.095-0.23485.605-0.39640.332-0.0697-0.44130.19070.1407-1.2524-0.291-0.04690.9223-0.0885-0.02921.058-0.04830.5371-125.005832.2306-66.4719
475.86981.22521.88654.75941.90247.58490.4499-0.2002-0.2349-0.3311-0.0110.36390.0510.4397-0.35640.3628-0.03290.03270.2672-0.06060.5741-117.616825.3743-56.2503
483.8545-1.22230.55654.91392.13668.9215-0.1806-0.43970.14270.29950.034-0.3064-0.3138-0.56790.16030.3298-0.0108-0.13980.6227-0.12520.3646-114.071829.8824-40.1834
491.2214-0.77212.36915.18251.78466.88820.18240.0692-0.647-0.25280.3745-1.39960.12571.7166-0.69550.5257-0.1701-0.08551.3649-0.19341.0618-97.661727.8049-30.803
501.86890.97762.74440.66962.22227.88291.0333-0.6952-0.29441.3569-0.1496-0.9750.89290.9249-0.98561.2089-0.0811-0.4661.1098-0.01991.1684-93.347429.3386-2.9963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 34 )A7 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 66 )A35 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 154 )A67 - 154
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 174 )A155 - 174
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 234 )A175 - 234
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 332 )A235 - 332
7X-RAY DIFFRACTION7chain 'A' and (resid 333 through 367 )A333 - 367
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 90 )B6 - 90
9X-RAY DIFFRACTION9chain 'B' and (resid 91 through 154 )B91 - 154
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 274 )B155 - 274
11X-RAY DIFFRACTION11chain 'B' and (resid 275 through 367 )B275 - 367
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 116 )C6 - 116
13X-RAY DIFFRACTION13chain 'C' and (resid 117 through 366 )C117 - 366
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 34 )D7 - 34
15X-RAY DIFFRACTION15chain 'D' and (resid 35 through 66 )D35 - 66
16X-RAY DIFFRACTION16chain 'D' and (resid 67 through 116 )D67 - 116
17X-RAY DIFFRACTION17chain 'D' and (resid 117 through 154 )D117 - 154
18X-RAY DIFFRACTION18chain 'D' and (resid 155 through 194 )D155 - 194
19X-RAY DIFFRACTION19chain 'D' and (resid 195 through 234 )D195 - 234
20X-RAY DIFFRACTION20chain 'D' and (resid 235 through 274 )D235 - 274
21X-RAY DIFFRACTION21chain 'D' and (resid 275 through 294 )D275 - 294
22X-RAY DIFFRACTION22chain 'D' and (resid 295 through 332 )D295 - 332
23X-RAY DIFFRACTION23chain 'D' and (resid 333 through 356 )D333 - 356
24X-RAY DIFFRACTION24chain 'E' and (resid 8 through 42 )E8 - 42
25X-RAY DIFFRACTION25chain 'E' and (resid 43 through 134 )E43 - 134
26X-RAY DIFFRACTION26chain 'E' and (resid 135 through 174 )E135 - 174
27X-RAY DIFFRACTION27chain 'E' and (resid 175 through 254 )E175 - 254
28X-RAY DIFFRACTION28chain 'E' and (resid 255 through 332 )E255 - 332
29X-RAY DIFFRACTION29chain 'E' and (resid 333 through 365 )E333 - 365
30X-RAY DIFFRACTION30chain 'F' and (resid 3 through 116 )F3 - 116
31X-RAY DIFFRACTION31chain 'F' and (resid 117 through 332 )F117 - 332
32X-RAY DIFFRACTION32chain 'F' and (resid 333 through 368 )F333 - 368
33X-RAY DIFFRACTION33chain 'G' and (resid 6 through 42 )G6 - 42
34X-RAY DIFFRACTION34chain 'G' and (resid 43 through 76 )G43 - 76
35X-RAY DIFFRACTION35chain 'G' and (resid 77 through 116 )G77 - 116
36X-RAY DIFFRACTION36chain 'G' and (resid 117 through 194 )G117 - 194
37X-RAY DIFFRACTION37chain 'G' and (resid 195 through 254 )G195 - 254
38X-RAY DIFFRACTION38chain 'G' and (resid 255 through 368 )G255 - 368
39X-RAY DIFFRACTION39chain 'H' and (resid 8 through 154 )H8 - 154
40X-RAY DIFFRACTION40chain 'H' and (resid 155 through 369 )H155 - 369
41X-RAY DIFFRACTION41chain 'I' and (resid 6 through 48 )I6 - 48
42X-RAY DIFFRACTION42chain 'I' and (resid 49 through 86 )I49 - 86
43X-RAY DIFFRACTION43chain 'I' and (resid 87 through 116 )I87 - 116
44X-RAY DIFFRACTION44chain 'I' and (resid 117 through 154 )I117 - 154
45X-RAY DIFFRACTION45chain 'I' and (resid 155 through 174 )I155 - 174
46X-RAY DIFFRACTION46chain 'I' and (resid 175 through 194 )I175 - 194
47X-RAY DIFFRACTION47chain 'I' and (resid 195 through 234 )I195 - 234
48X-RAY DIFFRACTION48chain 'I' and (resid 235 through 294 )I235 - 294
49X-RAY DIFFRACTION49chain 'I' and (resid 295 through 332 )I295 - 332
50X-RAY DIFFRACTION50chain 'I' and (resid 333 through 367 )I333 - 367

+
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://pdbjlvh1.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