[English] 日本語
Yorodumi
- PDB-6cgg: Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cgg
TitleAminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Arbekacin
ComponentsBifunctional AAC/APH
KeywordsTRANSFERASE / Kinase / Antibiotic / Aminoglycoside / Resistance / TRANSFERASE-Antibiotic complex
Function / homology
Function and homology information


aminoglycoside phosphotransferase activity / aminoglycoside 2''-phosphotransferase / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phosphorylation / response to antibiotic / ATP binding / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) domain / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Acetyltransferase (GNAT) domain / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Arbekacin / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Bifunctional AAC/APH
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsCaldwell, S.J. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-13107 Canada
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Plasticity of Aminoglycoside Binding to Antibiotic Kinase APH(2′′)-Ia.
Authors: Caldwell, S.J. / Berghuis, A.M.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional AAC/APH
B: Bifunctional AAC/APH
C: Bifunctional AAC/APH
D: Bifunctional AAC/APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,47223
Polymers143,7934
Non-polymers3,67919
Water12,899716
1
A: Bifunctional AAC/APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5545
Polymers35,9481
Non-polymers6064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional AAC/APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1997
Polymers35,9481
Non-polymers1,2516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bifunctional AAC/APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5545
Polymers35,9481
Non-polymers6064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bifunctional AAC/APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1646
Polymers35,9481
Non-polymers1,2165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.330, 99.780, 93.510
Angle α, β, γ (deg.)90.00, 105.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASPASPAA182 - 4798 - 305
21ASNASNASPASPBB182 - 4798 - 305
12THRTHRLYSLYSAA184 - 47810 - 304
22THRTHRLYSLYSCC184 - 47810 - 304
13ASNASNTHRTHRAA182 - 4768 - 302
23ASNASNTHRTHRDD182 - 4768 - 302
14THRTHRLYSLYSBB184 - 47810 - 304
24THRTHRLYSLYSCC184 - 47810 - 304
15ASNASNTHRTHRBB182 - 4768 - 302
25ASNASNTHRTHRDD182 - 4768 - 302
16THRTHRARGARGCC184 - 47510 - 301
26THRTHRARGARGDD184 - 47510 - 301

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Bifunctional AAC/APH


Mass: 35948.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: aacA-aphD, R015, VRA0030 / Plasmid: pET-22b-APH(2'')-Ia / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(LDE3)
References: UniProt: P0A0C1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, aminoglycoside 2''-phosphotransferase

-
Non-polymers , 6 types, 735 molecules

#2: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-84G / Arbekacin / (2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide / Arbekacin


Mass: 552.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C22H44N6O10 / Comment: antibiotic*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 80-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 23, 2016
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→99.78 Å / Num. obs: 62642 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 40.53 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.098 / Rrim(I) all: 0.142 / Net I/σ(I): 6.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.024 / Mean I/σ(I) obs: 1 / Num. unique obs: 4597 / CC1/2: 0.383 / Rpim(I) all: 0.793 / Rrim(I) all: 1.198 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLM0.1.27data reduction
Aimless0.3.11data scaling
Coot0.7.2model building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB 5IQA

5iqa


Resolution: 2.4→90.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 3153 5 %RANDOM
Rwork0.17798 ---
obs0.18026 59461 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.621 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.4→90.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9627 0 227 716 10570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01910040
X-RAY DIFFRACTIONr_bond_other_d00.028947
X-RAY DIFFRACTIONr_angle_refined_deg1.911.9713584
X-RAY DIFFRACTIONr_angle_other_deg3.747320867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24451159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40925.677532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.366151811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0261532
X-RAY DIFFRACTIONr_chiral_restr0.1150.21492
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211201
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021991
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4932.5764665
X-RAY DIFFRACTIONr_mcbond_other1.4932.5754663
X-RAY DIFFRACTIONr_mcangle_it2.4153.8565813
X-RAY DIFFRACTIONr_mcangle_other2.4153.8565814
X-RAY DIFFRACTIONr_scbond_it1.9082.7455375
X-RAY DIFFRACTIONr_scbond_other1.9042.7455375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0924.0437772
X-RAY DIFFRACTIONr_long_range_B_refined6.82431.25511744
X-RAY DIFFRACTIONr_long_range_B_other6.82431.25411744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A195200.08
12B195200.08
21A192300.07
22C192300.07
31A189200.09
32D189200.09
41B191080.08
42C191080.08
51B191740.06
52D191740.06
61C186500.09
62D186500.09
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 220 -
Rwork0.327 4359 -
obs--99.87 %
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)
12.10822.27851.42838.4855-3.25784.7991-0.30720.21050.4023-1.03370.20090.6360.32450.18230.10620.4016-0.0116-0.02520.41510.02220.191246.298-3.0355.357
20.35320.8212-0.68865.8088-3.98982.8077-0.06790.0088-0.1993-0.21840.5961.04660.1615-0.3974-0.52810.5488-0.01760.04790.59960.05730.748944.518-2.4736.126
32.8238-0.0081.76143.4558-1.84828.29810.0491-0.02850.1138-0.3329-0.1896-0.28680.01340.44150.14050.25380.01820.06880.42820.03410.05654.4462.3651.048
421.9038-3.2247-4.01993.31861.29555.682-0.0273-0.2284-0.5266-0.17720.08011.13190.0354-0.3722-0.05280.433-0.0215-0.11760.41050.02790.488441.5370.1549.492
56.6415-8.4239-0.343815.7788-0.89560.3673-0.6416-0.4503-0.2919-0.64030.4211-0.34940.41290.04050.22050.6302-0.02850.11810.6281-0.03140.516341.76113.42351.926
64.0307-1.2091-0.62436.4446-1.37122.89180.0964-0.0024-0.1802-0.0235-0.14840.3950.0002-0.01810.05190.2087-0.0583-0.01380.3460.00010.033145.671-6.02570.607
75.4251-2.56031.29932.79-0.5472.18710.0247-0.03080.40870.2023-0.10460.0898-0.34710.02910.07990.3853-0.02810.08440.3197-0.03050.087128.54410.97670.814
811.76114.5616-3.87027.4056-3.20316.9026-0.24520.4755-0.3242-0.64290.1034-0.42950.41620.08320.14190.3950.06870.02740.3897-0.09250.218723.6446.00858.889
919.724-2.36737.25214.7645-4.19355.13240.2165-1.1098-0.50550.0387-0.2135-0.18240.0118-0.1483-0.00310.40940.01980.00040.3401-0.01810.14536.7764.73220.755
103.55244.4161-6.10855.4952-7.597210.50630.1509-0.01490.07010.234-0.00750.1176-0.28760.0121-0.14350.52960.06630.06260.38430.01790.486437.736-7.30215.342
1117.31698.3996-6.671911.6751-7.00264.43750.12790.3034-1.0921-0.6102-0.17680.24530.27980.04890.04890.57720.0078-0.01290.4453-0.0250.418337.9814.80239.813
121.9835-0.11460.41592.3402-0.96547.9599-0.0238-0.26040.20890.13180.005-0.0044-0.54670.07140.01880.45420.0639-0.02070.2205-0.03750.085242.96812.91123.895
130.7617-1.6379-1.560216.54311.77623.5062-0.1034-0.0796-0.3039-0.5629-0.22721.20050.3930.16570.33060.455-0.0157-0.02680.44830.05210.626339.7270.42126.831
144.9169-11.1399-4.335925.71579.97593.8724-0.05030.19560.06720.09620.02340.11730.0287-0.02230.02690.5284-0.0808-0.00430.57090.08070.497754.0871.9523.498
156.3789-1.72050.51493.28130.16542.1557-0.1260.0839-0.31780.05720.15880.33680.0161-0.2065-0.03290.28760.0257-0.03070.20510.02150.044633.832.815.488
162.0333-1.88230.38065.5176-1.57192.12490.06250.1037-0.1723-0.0466-0.16880.13220.0143-0.04310.10620.2302-0.01890.01450.2501-0.09120.049949.882-15.0787.571
175.48792.09784.232310.6692.88737.7380.2823-0.76420.49111.1496-0.49761.28170.0704-0.86510.21540.4533-0.06020.20130.3537-0.07060.271644.183-18.63119.788
189.22170.2367-3.50579.0051-1.84442.9151-0.38640.06410.0131-0.19120.1012-0.852-0.136-0.31730.28530.2936-0.0229-0.01080.368-0.08130.204363.89935.70574.408
1916.55115.4327-1.36232.71452.57739.9408-0.14830.11090.3058-0.20930.09410.1071-0.50730.19210.05410.59-0.05190.02470.52090.05830.567464.92834.24255.177
203.8839-0.6656-1.09743.25531.03957.877-0.03660.1144-0.0341-0.4098-0.04720.22710.2371-0.48930.08370.2394-0.0506-0.07350.4135-0.05380.205455.8730.14470.142
2120.1849-8.66971.09436.92832.88595.93320.0311-0.29640.4654-0.45340.1092-0.86320.04930.2428-0.14030.41160.00890.11980.40770.04950.413468.77132.34668.843
2200000000000000-00.3927000.392700.3927000
233.0946-1.50930.94025.6721-2.16495.0771-0.132-0.18340.26450.2650.0122-0.1426-0.3902-0.16730.11980.2180.0503-0.07010.3784-0.08060.133164.00839.23389.513
244.4897-2.101-2.19092.56810.52372.3464-0.2765-0.0274-0.38820.02130.08470.26070.2033-0.22720.19190.28870.0043-0.0230.2152-0.0190.046881.59422.34391.198
258.49891.621.29137.02713.48048.4399-0.15750.39210.3724-0.5383-0.16140.7906-0.1419-0.6330.31880.26040.0048-0.00280.32890.02380.113386.38925.84878.697
2617.3271-1.641-4.44062.46662.43732.9003-0.2631-0.4601-0.13130.10940.17150.08960.12730.20360.09160.40850.0089-0.01330.41970.03220.3374.46728.68440.497
270.2137-0.3731.39477.21213.127614.0175-0.14590.05740.15080.878-0.5121-0.826-0.4230.25110.65790.44560.0026-0.05010.55610.04720.517373.21341.18335.401
281.32853.8780.791912.10872.54170.5395-0.09050.03820.1968-0.12410.1736-0.109-0.01660.0525-0.0830.5428-0.003-0.05220.5695-0.06160.635272.71228.4759.235
292.4122-0.3313-1.40393.2058-0.68168.1817-0.0558-0.1042-0.335-0.0439-0.0222-0.04720.1093-0.1090.0780.392-0.008-0.05470.4426-0.02120.31868.35920.1443.093
3012.911-5.79582.45574.77650.22315.95460.07870.42050.8337-0.3736-0.233-0.6257-0.2275-0.07910.15430.49860.0008-0.03450.44710.01840.517472.70930.28146.657
3139.462730.4024-30.836223.4235-23.757324.09620.2912-0.26650.07010.2406-0.22160.0629-0.23390.2206-0.06950.59030.072-0.05190.553-0.08180.651857.98130.44640.55
327.17-0.17870.29433.0579-1.13152.3284-0.04090.2713-0.1579-0.2435-0.0415-0.40390.19860.23390.08240.37520.00370.04710.5109-0.07650.140177.98931.47225.526
334.2262-2.95-1.18166.81370.91761.8599-0.08870.12030.58150.30010.1935-0.2361-0.08140.1317-0.10490.3463-0.0305-0.10440.51290.06690.13761.64948.87127.822
349.314.9017-4.75326.3306-1.688911.1205-0.1619-0.7450.33591.05330.069-0.80250.11820.81170.09290.66540.1077-0.20060.7225-0.03960.394366.61151.42840.759
3500000000000000-00.3927000.392700.3927000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A500
2X-RAY DIFFRACTION1A700 - 702
3X-RAY DIFFRACTION1A900 - 915
4X-RAY DIFFRACTION2A175 - 187
5X-RAY DIFFRACTION3A188 - 207
6X-RAY DIFFRACTION3A217 - 229
7X-RAY DIFFRACTION3A237 - 277
8X-RAY DIFFRACTION4A208 - 216
9X-RAY DIFFRACTION5A230 - 236
10X-RAY DIFFRACTION6A278 - 318
11X-RAY DIFFRACTION6A367 - 431
12X-RAY DIFFRACTION7A319 - 366
13X-RAY DIFFRACTION7A432 - 447
14X-RAY DIFFRACTION8A448 - 479
15X-RAY DIFFRACTION9B500
16X-RAY DIFFRACTION9B700 - 702
17X-RAY DIFFRACTION9B900 - 915
18X-RAY DIFFRACTION10B600
19X-RAY DIFFRACTION11B175 - 187
20X-RAY DIFFRACTION12B188 - 207
21X-RAY DIFFRACTION12B217 - 229
22X-RAY DIFFRACTION12B237 - 277
23X-RAY DIFFRACTION13B208 - 216
24X-RAY DIFFRACTION14B230 - 236
25X-RAY DIFFRACTION15B278 - 318
26X-RAY DIFFRACTION15B367 - 431
27X-RAY DIFFRACTION16B319 - 366
28X-RAY DIFFRACTION16B432 - 447
29X-RAY DIFFRACTION17B448 - 479
30X-RAY DIFFRACTION18C500
31X-RAY DIFFRACTION18C700 - 702
32X-RAY DIFFRACTION18C900 - 915
33X-RAY DIFFRACTION19C175 - 187
34X-RAY DIFFRACTION20C188 - 207
35X-RAY DIFFRACTION20C217 - 229
36X-RAY DIFFRACTION20C237 - 277
37X-RAY DIFFRACTION21C208 - 216
38X-RAY DIFFRACTION22C230 - 236
39X-RAY DIFFRACTION23C278 - 318
40X-RAY DIFFRACTION23C367 - 431
41X-RAY DIFFRACTION24C319 - 366
42X-RAY DIFFRACTION24C432 - 447
43X-RAY DIFFRACTION25C448 - 479
44X-RAY DIFFRACTION26D500
45X-RAY DIFFRACTION26D700 - 702
46X-RAY DIFFRACTION26D900 - 915
47X-RAY DIFFRACTION27D600
48X-RAY DIFFRACTION28D175 - 187
49X-RAY DIFFRACTION29D188 - 207
50X-RAY DIFFRACTION29D217 - 229
51X-RAY DIFFRACTION29D237 - 277
52X-RAY DIFFRACTION30D208 - 216
53X-RAY DIFFRACTION31D230 - 236
54X-RAY DIFFRACTION32D278 - 318
55X-RAY DIFFRACTION32D367 - 431
56X-RAY DIFFRACTION33D319 - 366
57X-RAY DIFFRACTION33D432 - 447
58X-RAY DIFFRACTION34D448 - 479

+
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