[English] 日本語
Yorodumi
- PDB-5k8f: Crystal structure of Acetyl-CoA Synthetase in complex with ATP an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k8f
TitleCrystal structure of Acetyl-CoA Synthetase in complex with ATP and Acetyl-AMP from Cryptococcus neoformans H99
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / NIH / NIAID / Synthetase / ACS1 / Acetyl-AMP / ATP / Adenosine TriPhosphate / Acetyl Adenylate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding / metal ion binding
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6R9 / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Delker, S.L. / Potts, K.T. / Lorimer, D.D. / Edwards, T.E. / Mutz, M.W.
CitationJournal: To Be Published
Title: Crystal structure of Acetyl-CoA Synthetase in complex with ATP and Acetyl-AMP from Cryptococcus neoformans H99
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Delker, S.L. / Potts, K.T. / Numa, M.M. / Edwards, T.E. / Lorimer, D.D. / Mutz, M.W. / Krysan, D.J.
History
DepositionMay 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 2.0Apr 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / citation_author / diffrn / entity / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_prerelease_seq / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight ..._diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _reflns.B_iso_Wilson_estimate / _reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_redundancy / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq_dif.details / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Ligand identity
Details: Removed low occupancy Mg atom and alt loop conformation near ATP.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,86723
Polymers232,4273
Non-polymers3,44020
Water6,684371
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6458
Polymers77,4761
Non-polymers1,1697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5837
Polymers77,4761
Non-polymers1,1076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6408
Polymers77,4761
Non-polymers1,1647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.370, 83.920, 101.570
Angle α, β, γ (deg.)110.060, 105.240, 87.650
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Acetyl-coenzyme A synthetase


Mass: 77475.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_00797 / Plasmid: PEMB7013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J9VFT1, acetate-CoA ligase

-
Non-polymers , 6 types, 391 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-6R9 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate


Mass: 389.258 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H16N5O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: ACETYL COA SYNTHETASE FROM CRYPTOCOCCUS NEOFORMANS (CRNEC.00629.A.FS11.PD00402) AT 10MG/ ML (IN 10 MM TRIS, PH = 7.5, 20 MM NACL) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. 1MM ATP ...Details: ACETYL COA SYNTHETASE FROM CRYPTOCOCCUS NEOFORMANS (CRNEC.00629.A.FS11.PD00402) AT 10MG/ ML (IN 10 MM TRIS, PH = 7.5, 20 MM NACL) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. 1MM ATP AND 1MM MGCL2 WERE ADDED TO THE PROTEIN SOLUTION AND INCUBATED FOR 5 MINUTES BEFORE SETTING UP TRIALS. CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND IN WIZARD 1 AND 2 SCREEN CONDITION E8 (10% W/V PEG8,000, 0.1M NA/K PHOSPHATE PH6.2) AND CRYO-PROTECTED IN 20% ETHYLENE GLYCOL. CRYSTAL ID 271854A7 GJX4-8 APS21-ID-G), PH 6.20, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 6.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 77299 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 37.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.088 / Χ2: 0.975 / Net I/σ(I): 14.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.510.5172.5656460.8610.59797.8
2.51-2.580.4512.9755240.8820.52197.7
2.58-2.660.3783.554010.9170.43798.2
2.66-2.740.3174.2552760.940.36698.1
2.74-2.830.265.1150860.9560.398.3
2.83-2.930.2036.4748880.9710.23598.2
2.93-3.040.1717.7347840.9770.19798.3
3.04-3.160.12510.1145970.9870.14498.6
3.16-3.30.09413.2143850.9920.10998.5
3.3-3.460.07516.3742420.9950.08798.8
3.46-3.650.06219.239690.9960.07298.6
3.65-3.870.05521.4738230.9970.06498.9
3.87-4.140.04624.9135740.9970.05399
4.14-4.470.0428.4433380.9980.04798.9
4.47-4.90.03730.5530530.9980.04299.2
4.9-5.480.03730.8327620.9980.04399
5.48-6.330.03830.0924540.9980.04499.4
6.33-7.750.03432.8120650.9980.0499
7.75-10.960.02739.1215770.9990.03198.9
10.96-500.02637.368550.9990.03196.5

-
Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFI
Resolution: 2.45→26.62 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 1997 2.59 %
Rwork0.1879 75209 -
obs0.1889 77206 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.47 Å2 / Biso mean: 52.7124 Å2 / Biso min: 20.5 Å2
Refinement stepCycle: final / Resolution: 2.45→26.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14907 0 216 377 15500
Biso mean--49.38 39.02 -
Num. residues----1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215682
X-RAY DIFFRACTIONf_angle_d0.46721462
X-RAY DIFFRACTIONf_dihedral_angle_d12.7025484
X-RAY DIFFRACTIONf_chiral_restr0.0422329
X-RAY DIFFRACTIONf_plane_restr0.0042766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.510.27811400.26025301544198
2.51-2.580.26461420.24795315545798
2.58-2.650.30861420.23995355549798
2.65-2.740.29091430.24455374551798
2.74-2.840.27841420.23595355549798
2.84-2.950.26481420.22615342548498
2.95-3.090.25921440.22215418556299
3.09-3.250.24321430.21785372551599
3.25-3.450.2271420.20175371551399
3.45-3.720.22361440.18245408555299
3.72-4.090.20481430.16735377552099
4.09-4.680.19871450.14595439558499
4.68-5.880.18491430.15215403554699
5.89-26.620.18371420.16115379552199
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)
12.0538-0.4756-0.88011.0730.18591.7920.08370.06980.139-0.1861-0.08260.011-0.1952-0.1454-0.00580.2097-0.0037-0.04710.1728-0.02030.2236-9.424112.3094-2.3171
22.6637-0.6995-1.38110.7992-0.29132.93360.1147-0.07930.1177-0.1123-0.1536-0.1195-0.25850.14520.03610.2076-0.0141-0.02530.1472-0.01380.2572-0.559212.1362-4.8149
32.1924-0.5648-0.76951.19640.45861.83730.11160.21340.2086-0.1634-0.08660.1569-0.3071-0.4792-0.02960.21680.0604-0.03950.30370.00420.3283-19.748420.88611.9543
43.1221-0.4888-0.22517.0624-1.63482.66810.24660.10280.8893-0.0938-0.266-0.8349-0.8308-0.12970.03330.60120.1901-0.0050.462-0.05310.7257-19.715141.89418.6471
50.9516-0.16070.361.2036-0.33021.5146-0.2418-0.6045-0.53140.34860.20090.18210.5324-0.1401-0.1120.54160.11430.15680.60690.28440.53527.6847-20.615629.356
61.52770.2020.22611.4021-0.061.2183-0.2219-0.47920.05820.22080.2266-0.12230.02980.2752-0.00050.22850.0815-0.04120.4698-0.01440.257317.96855.034522.198
70.02750.36090.09496.0786-0.69244.8247-0.1243-0.6391-0.45330.24330.2785-0.46490.41590.3542-0.26430.36270.16060.04710.50320.13830.373917.4983-14.695522.3884
80.94150.23220.16981.3622-0.59631.2426-0.2296-0.7271-0.34360.6030.2346-0.06580.2672-0.1229-0.01190.65190.24960.0640.84290.2710.448816.504-17.27440.0888
91.0626-0.46790.59182.264-0.73922.24580.1271-0.4807-0.39110.1423-0.0033-0.09240.64320.4251-0.15170.61180.21780.06750.5720.22260.598327.8289-27.148725.9459
102.89611.49870.98581.28662.00416.4632-0.6886-0.3808-0.03570.45670.5518-0.3407-0.56880.12320.07720.92510.3039-0.11720.98490.13540.57840.447-18.720646.0254
110.6742-0.1046-0.78321.00320.24510.9287-0.44190.4061-0.6536-0.2308-0.17250.01560.8353-0.38650.20961.1092-0.36370.32220.6214-0.35530.93860.4643-35.4285-30.7547
121.3302-0.2387-0.08650.72-0.0641.8551-0.1503-0.0183-0.2935-0.0722-0.04-0.15130.48540.30.14820.41960.07640.11360.22290.04110.407220.5449-15.964-8.6875
130.97790.06420.09990.89610.1181.1316-0.34010.3716-0.6463-0.1311-0.01410.02620.91990.10580.140.85060.0260.2660.2743-0.09620.615615.8214-29.3228-23.9256
141.8007-0.462-0.42484.670.50252.2848-0.0120.5516-0.2099-0.5175-0.31760.52930.2999-0.58780.2520.4191-0.02410.0220.414-0.11990.31011.6291-11.7892-31.2927
155.1275-0.23453.04363.24830.73292.84990.05650.64480.0333-0.8419-0.5153-0.00450.3414-0.2250.48420.8557-0.03860.18870.5108-0.17830.496312.379-21.8216-44.8553
166.33360.13010.80213.53570.75816.7650.03440.6167-0.4478-0.07670.1576-0.2341-0.3020.7386-0.17380.7889-0.0170.20410.6329-0.10190.471725.8537-20.7034-48.4122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 245 )A11 - 245
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 317 )A246 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 526 )A318 - 526
4X-RAY DIFFRACTION4chain 'A' and (resid 527 through 681 )A527 - 681
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 132 )B11 - 132
6X-RAY DIFFRACTION6chain 'B' and (resid 133 through 278 )B133 - 278
7X-RAY DIFFRACTION7chain 'B' and (resid 279 through 317 )B279 - 317
8X-RAY DIFFRACTION8chain 'B' and (resid 318 through 493 )B318 - 493
9X-RAY DIFFRACTION9chain 'B' and (resid 494 through 555 )B494 - 555
10X-RAY DIFFRACTION10chain 'B' and (resid 556 through 681 )B556 - 681
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 63 )C11 - 63
12X-RAY DIFFRACTION12chain 'C' and (resid 64 through 278 )C64 - 278
13X-RAY DIFFRACTION13chain 'C' and (resid 279 through 463 )C279 - 463
14X-RAY DIFFRACTION14chain 'C' and (resid 464 through 526 )C464 - 526
15X-RAY DIFFRACTION15chain 'C' and (resid 527 through 579 )C527 - 579
16X-RAY DIFFRACTION16chain 'C' and (resid 580 through 681 )C580 - 681

+
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