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- PDB-2x2h: Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- ... -

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Basic information

Entry
Database: PDB / ID: 2x2h
TitleCrystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase
ComponentsALPHA-1,4-GLUCAN LYASE ISOZYME 1
KeywordsLYASE / ANHYDROFRUCTOSE PATHWAY / GLYCOSIDE HYDROLASE FAMILY 31 / STARCH BINDING DOMAIN
Function / homology
Function and homology information


exo-(1,4)-alpha-D-glucan lyase activity / glucosidase II complex / alpha-glucosidase activity / N-glycan processing / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
glycosyl hydrolase (family 31) / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like ...glycosyl hydrolase (family 31) / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Glucosidase II subunit alpha
Similarity search - Component
Biological speciesGRACILARIOPSIS LEMANEIFORMIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsRozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure of Alpha-1,4-Glucan Lyase, a Unique Glycoside Hydrolase Family Member with a Novel Catalytic Mechanism.
Authors: Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Zhang, R. / Dijkstra, B.W.
History
DepositionJan 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references / Non-polymer description ...Database references / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp
Revision 1.5Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
B: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
C: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
D: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,32431
Polymers464,2494
Non-polymers2,07627
Water66,4573689
1
A: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,97813
Polymers116,0621
Non-polymers91612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3745
Polymers116,0621
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5167
Polymers116,0621
Non-polymers4536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4576
Polymers116,0621
Non-polymers3945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.678, 96.629, 134.457
Angle α, β, γ (deg.)80.54, 83.28, 85.26
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 6 / Auth seq-ID: 14 - 1038 / Label seq-ID: 3 - 1027

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(0.2718, -0.6506, 0.7091), (0.6725, 0.6554, 0.3436), (-0.6883, 0.3835, 0.6157)-7.778, 3.747, 76.03
2given(0.2703, -0.6521, 0.7083), (-0.6611, -0.6605, -0.3558), (0.6999, -0.3721, -0.6097)30.19, -1.888, -55.26
3given(1, 0.002044, 0.005377), (0.002, -1, 0.008123), (0.005393, -0.008112, -1)53.87, 2.778, 20.89

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Components

#1: Protein
ALPHA-1,4-GLUCAN LYASE ISOZYME 1


Mass: 116062.156 Da / Num. of mol.: 4 / Fragment: RESIDUES 62-1088
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GRACILARIOPSIS LEMANEIFORMIS (eukaryote)
Description: REPLICATING VECTOR WITH HARS SEQUENCE. COLLECTED AT TAPING BAY, TSINGTAO, CHINA
Production host: PICHIA ANGUSTA (fungus) / Strain (production host): RB11 / References: UniProt: Q9STC1, EC: 4.2.2.13
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3689 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 50 AMINO ACIDS ARE A SIGNAL PEPTIDE. THE NEXT 11 AMINO ACIDS ARE NOT PRESENT IN THE ENZYME.

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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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18-21% PEG 8000, 0.1 M SODIUM ACETATE, PH 5.0-5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9762
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 258096 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.14
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.9 / % possible all: 76.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G3M
Resolution: 2.06→132.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.597 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21453 12978 5 %RANDOM
Rwork0.16834 ---
obs0.17068 245106 92.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20.45 Å20.99 Å2
2---1.9 Å22.23 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.06→132.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32648 0 134 3689 36471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02233651
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.92945745
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6825.0194108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00924.6261805
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.591155139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.20115188
X-RAY DIFFRACTIONr_chiral_restr0.0780.24681
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02126872
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.599220340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.001332779
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.666213311
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.993312964
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8128 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.425
2Bloose positional0.295
3Cloose positional0.325
4Dloose positional0.35
1Aloose thermal2.5910
2Bloose thermal2.9910
3Cloose thermal1.6810
4Dloose thermal2.0610
LS refinement shellResolution: 2.061→2.115 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 737 -
Rwork0.221 13307 -
obs--68.33 %
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)
10.32390.19770.15230.9471-0.33570.61310.00960.09-0.0683-0.14610.01280.03080.10330.015-0.02240.0991-0.0331-0.01390.109-0.03390.1113-11.7267-53.0026-3.8736
21.09320.3377-0.0380.7538-0.18230.2660.0366-0.0863-0.12490.0685-0.0355-0.0520.0269-0.0324-0.00110.0735-0.0138-0.01340.05530.00120.0876-0.2158-53.07777.3179
30.52470.17570.07950.8896-0.22150.6034-0.0001-0.04970.0460.034-0.0030.1281-0.0441-0.09530.00310.0597-0.00610.00740.0866-0.02450.0804-10.867-32.73220.0064
40.40120.1149-0.05060.467-0.0870.11590.00040.04450.0005-0.0599-0.005-0.01650.0063-0.01380.00460.0885-0.0087-0.00240.0848-0.02720.06696.4512-26.1087-13.9359
51.31490.77630.2481.3350.14280.5186-0.02110.2312-0.0526-0.20820.0498-0.05780.0869-0.0239-0.02870.15160.01040.0260.1315-0.02040.0333.8202-33.3415-30.6039
61.1170.05980.09221.1141-0.00841.03020.00560.18860.002-0.17510.01150.08470.051-0.1019-0.01710.1065-0.0248-0.00730.0975-0.01870.0429-9.5108-37.6988-21.7345
70.4598-0.00440.09570.4883-0.0790.4587-0.0056-0.01340.04940.0162-0.0007-0.0047-0.0316-0.00960.00630.0802-0.00950.01010.0752-0.02230.08516.5271-16.4062-2.8155
80.6606-0.13220.22510.76310.32360.902-0.0257-0.03670.03720.0932-0.0162-0.13440.01440.12210.04190.0722-0.02410.00020.0844-0.00330.135129.2941-17.82913.8117
90.7210.69210.13231.7221-0.29661.7789-0.0361-0.07980.11850.0836-0.046-0.314-0.11780.29370.08220.0763-0.0393-0.050.1261-0.02060.222736.549-8.34137.5669
100.6608-0.10030.0310.6703-0.39560.6850.05170.1111-0.088-0.2162-0.0811-0.11810.19130.14840.02940.24730.10010.02520.20710.00580.103625.1496-33.748357.2902
110.825-0.29560.1960.969-0.18250.37250.0347-0.0342-0.0236-0.0243-0.0526-0.10130.0920.13320.0180.16970.03070.00060.19170.02670.050218.5597-26.215970.1869
120.2633-0.19580.05410.4597-0.19620.35070.04960.0257-0.0131-0.0982-0.03030.02830.09920.0347-0.01930.1670.0136-0.00930.15360.00070.0740.1337-12.986352.4363
130.6228-0.33650.17392.4244-0.58050.63670.11210.0858-0.1379-0.2655-0.00590.19520.2913-0.0432-0.10620.3030.026-0.08160.2011-0.03130.0698-6.5377-28.903141.4757
141.42090.13680.08521.2357-0.33891.38790.07760.0805-0.1473-0.23220.00220.16360.3585-0.0292-0.07980.27880.0319-0.06680.1164-0.00280.0818-1.0168-35.267354.5603
150.6437-0.14530.12510.5754-0.23580.49280.0232-0.00710.0258-0.0091-0.02450.03050.03060.03490.00140.13670.0009-0.00110.14580.0070.06971.737-5.336162.1844
160.6992-0.00330.01940.6950.04540.8529-0.0045-0.01240.15660.0167-0.0195-0.0256-0.06920.09860.02390.1297-0.0044-0.00470.14940.02020.13199.72348.799158.8435
171.08190.0915-0.06181.1384-0.20680.9098-0.0008-0.03150.16080.0208-0.021-0.1269-0.13280.20940.02180.1386-0.04410.01190.20320.05580.199919.734818.306153.399
181.5233-0.18180.39451.9033-0.37681.16790.09310.12140.3852-0.0948-0.0745-0.0781-0.24080.1719-0.01860.1655-0.0529-0.00070.14350.06130.218913.32425.355751.9757
191.70290.6162-0.49670.9211-0.05450.20790.1034-0.06530.28940.1134-0.00450.0245-0.11170.0314-0.09890.2412-0.01570.0350.14780.02350.219953.121443.6154-42.6732
200.90730.1931-0.33930.6364-0.1780.51140.07160.01170.08370.0446-0.0825-0.131-0.08840.14060.01090.1446-0.0509-0.00190.151-0.00420.172769.10732.9655-40.4537
210.82440.122-0.17240.7773-0.05070.49360.02610.19560.0679-0.13150.01610.0151-0.0451-0.0064-0.04220.1341-0.01320.01330.14810.01680.084147.385824.4974-51.3583
220.55080.2625-0.16220.4528-0.16270.35040.02740.02480.03350.0387-0.00170.0096-0.0468-0.0079-0.02570.11640.00020.00430.0981-0.00910.094538.643115.7487-32.51
230.60510.3513-0.15492.2796-0.21770.50360.0866-0.06190.14240.17690.01470.108-0.1764-0.0535-0.10130.15250.00950.06510.1039-0.02490.083431.479428.6871-21.7063
241.5645-0.28290.28051.1177-0.43241.77060.0829-0.00140.25940.11960.00910.1133-0.2615-0.0853-0.0920.14920.00510.07320.07710.020.152437.066338.166-34.7202
250.75450.0584-0.07450.6227-0.10930.3960.00090.1301-0.0523-0.0560.0176-0.03260.0191-0.0206-0.01850.1123-0.01330.00950.1325-0.01740.096240.62145.2315-42.7018
260.9089-0.2110.02161.08330.32780.93140.01050.0088-0.19720.04020.0028-0.15580.1190.0993-0.01330.1203-0.0038-0.01410.1098-0.00010.18153.1286-10.6372-30.3229
271.21130.3310.07611.4194-0.08961.22090.0729-0.0188-0.38320.1727-0.0232-0.11330.29030.0825-0.04960.15710.009-0.00120.0749-0.02410.272251.0618-23.1428-30.8694
280.4992-0.291-0.09261.3075-0.83490.8723-0.0447-0.13570.07810.21290.10370.1248-0.1586-0.0142-0.0590.14920.02810.01260.1982-0.03180.191338.609152.372428.8184
290.9747-0.47110.13490.6892-0.19460.31450.03760.03050.1224-0.042-0.0121-0.0286-0.0344-0.0338-0.02550.084-0.0039-0.00010.0706-0.01770.101151.60356.755315.2116
300.6928-0.2674-0.11840.75020.0690.51420.00580.0403-0.0861-0.06470.01350.17580.0128-0.0844-0.01930.0803-0.0016-0.02440.1039-0.00760.125444.317836.516320.3055
310.2637-0.10430.05790.5265-0.1910.3528-0.0017-0.1183-0.02890.10.02390.01130.0046-0.026-0.02220.104-0.004-0.01580.1405-0.01020.077266.113422.489742.7059
321.5614-1.0991-0.05661.5733-0.14181.0721-0.0638-0.28840.01030.2540.15850.045-0.1923-0.1129-0.09470.20190.00870.01390.1951-0.03540.062755.837738.650952.9682
332.13070.212-0.10320.7734-0.08231.2644-0.0113-0.306-0.09960.20670.05960.1393-0.0929-0.1166-0.04830.12050.03370.02390.15520.00990.093944.430540.383742.9023
340.5085-0.0663-0.10020.531-0.15880.5083-0.0081-0.0137-0.0873-0.01650.02370.08790.039-0.0501-0.01560.0835-0.013-0.02360.095-0.02020.097460.45119.013323.7665
350.62230.0671-0.31411.00280.18950.5745-0.00350.0108-0.021-0.108-0.0255-0.1042-0.01450.07540.0290.07820.0116-0.01180.0868-0.01810.088483.23420.839417.3012
361.0434-0.4374-0.30821.51550.08541.3468-0.02240.0011-0.0402-0.10940.0063-0.31310.04650.19010.01610.08580.02130.01580.0535-0.01130.095990.543511.461213.7054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 66
2X-RAY DIFFRACTION2A67 - 178
3X-RAY DIFFRACTION3A179 - 284
4X-RAY DIFFRACTION4A285 - 447
5X-RAY DIFFRACTION5A448 - 550
6X-RAY DIFFRACTION6A551 - 621
7X-RAY DIFFRACTION7A622 - 884
8X-RAY DIFFRACTION8A885 - 984
9X-RAY DIFFRACTION9A985 - 1038
10X-RAY DIFFRACTION10B14 - 127
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