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- PDB-2v69: Crystal structure of Chlamydomonas reinhardtii Rubisco with a lar... -

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Basic information

Entry
Database: PDB / ID: 2v69
TitleCrystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E
Components(RIBULOSE BISPHOSPHATE CARBOXYLASE ...RuBisCO) x 2
KeywordsOXIDOREDUCTASE / LARGE SUBUNIT LOOP 6 MUTATION / CO2/O2 SPECIFICITY / CARBON DIOXIDE FIXATION / PHOTOSYNTHESIS / TRANSIT PEPTIDE / PHOTORESPIRATION / METAL-BINDING / HYDROXYLATION / METHYLATION / CHLOROPLAST / CALVIN CYCLE / MONOOXYGENASE / LYASE / RUBISCO / PLASTID / MAGNESIUM / ACETYLATION
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I ...Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKarkehabadi, S. / Satagopan, S. / Taylor, T.C. / Spreitzer, R.J. / Andersson, I.
CitationJournal: Biochemistry / Year: 2007
Title: Structural Analysis of Altered Large-Subunit Loop-6-Carboxy-Terminus Interactions that Influence Catalytic Efficiency and Co2-O2 Specificity of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase
Authors: Karkehabadi, S. / Satagopan, S. / Taylor, T.C. / Spreitzer, R.J. / Andersson, I.
History
DepositionJul 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
B: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
D: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
F: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
H: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
J: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
K: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
L: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
M: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
N: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
O: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
P: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,49056
Polymers551,95716
Non-polymers4,53340
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area124160 Å2
ΔGint-724.6 kcal/mol
Surface area155100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)114.242, 169.140, 137.179
Angle α, β, γ (deg.)90.00, 96.24, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12B
22A
13C
23A
14D
24A
15E
25A
16F
26A
17G
27A
18H
28A
19I
110J
210I
111K
211I
112L
212I
113M
213I
114N
214I
115O
215I
116P
216I

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A13 - 468
1211A476 - 477
1121B13 - 468
2121A13 - 468
1221B476 - 477
2221A476 - 477
1131C13 - 468
2131A13 - 468
1231C476 - 477
2231A476 - 477
1141D13 - 468
2141A13 - 468
1241D476 - 477
2241A476 - 477
1151E13 - 468
2151A13 - 468
1251E476 - 477
2251A476 - 477
1161F13 - 468
2161A13 - 468
1261F476 - 477
2261A476 - 477
1171G13 - 468
2171A13 - 468
1271G476 - 477
2271A476 - 477
1181H13 - 468
2181A13 - 468
1281H476 - 477
2281A476 - 477
1191I1 - 140
11101J1 - 140
21101I1 - 140
11111K1 - 140
21111I1 - 140
11121L1 - 140
21121I1 - 140
11131M1 - 140
21131I1 - 140
11141N1 - 140
21141I1 - 140
11151O1 - 140
21151I1 - 140
11161P1 - 140
21161I1 - 140

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.1965, -0.6713, -0.7147), (-0.6729, -0.6225, 0.3997), (-0.7132, 0.4024, -0.574)46.21, 17.25, 61.18
3given(0.00117, -0.5841, -0.8117), (0.6769, 0.5979, -0.4293), (0.7361, -0.5489, 0.3961)51.24, 11.42, 19.08
4given(0.9713, 0.03683, 0.2349), (0.03631, -0.9993, 0.006565), (0.235, 0.002153, -0.972)-8.496, 26.6, 67.72
5given(-0.9928, 0.09097, -0.07794), (0.09483, 0.1993, -0.9753), (-0.07319, -0.9757, -0.2065)29.31, 44.72, 57.91
6given(-0.2008, 0.5804, 0.7892), (0.5792, -0.5794, 0.5735), (0.7901, 0.5722, -0.2198)-19.77, -7.22, 25.08
7given(0.002765, 0.6745, 0.7383), (-0.5826, 0.6011, -0.547), (-0.8127, -0.4287, 0.3946)-22, 33.33, 39.05
8given(-0.9795, -0.1253, -0.1576), (-0.1307, -0.1999, 0.9711), (-0.1532, 0.9718, 0.1794)34.96, -16.71, 18.38
9given(0.1969, -0.6701, -0.7157), (-0.6746, -0.6223, 0.397), (-0.7115, 0.4046, -0.5746)46.2, 17.35, 61.14
10given(0.004787, -0.5843, -0.8115), (0.6787, 0.5979, -0.4265), (0.7344, -0.5487, 0.3994)51.19, 11.36, 19.02
11given(0.9722, 0.03173, 0.2318), (0.03084, -0.9995, 0.007487), (0.2319, -0.00013, -0.9727)-8.495, 26.75, 67.83
12given(-0.9923, 0.09459, -0.07952), (0.09731, 0.2016, -0.9746), (-0.07617, -0.9749, -0.2092)29.44, 44.75, 58.12
13given(-0.2032, 0.584, 0.7859), (0.5741, -0.5791, 0.5788), (0.7931, 0.5689, -0.2176)-19.49, -7.274, 24.95
14given(0.003392, 0.6781, 0.7349), (-0.5783, 0.6009, -0.5518), (-0.8158, -0.4231, 0.3942)-21.79, 33.41, 39.17
15given(-0.9795, -0.121, -0.1613), (-0.1349, -0.2015, 0.9702), (-0.1499, 0.972, 0.1811)35.14, -16.67, 18.24

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Components

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RIBULOSE BISPHOSPHATE CARBOXYLASE ... , 2 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RIBULOSE-1 / 5-BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RUBISCO LARGE SUBUNIT


Mass: 52710.867 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Strain: 2137 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P00877, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1 / RIBULOSE-1 / 5-BISPHOSPHATE CARBOXYLASE SMALL CHAIN / RUBISCO SMALL SUBUNIT 1


Mass: 16283.806 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Strain: 2137 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P00873, ribulose-bisphosphate carboxylase

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Sugars , 1 types, 8 molecules

#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharideCarbohydrate / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 3 types, 427 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 473 TO GLU ENGINEERED RESIDUE IN CHAIN B, ASP 473 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, ASP 473 TO GLU ENGINEERED RESIDUE IN CHAIN B, ASP 473 TO GLU ENGINEERED RESIDUE IN CHAIN C, ASP 473 TO GLU ENGINEERED RESIDUE IN CHAIN D, ASP 473 TO GLU ENGINEERED RESIDUE IN CHAIN E, ASP 473 TO GLU ENGINEERED RESIDUE IN CHAIN F, ASP 473 TO GLU ENGINEERED RESIDUE IN CHAIN G, ASP 473 TO GLU ENGINEERED RESIDUE IN CHAIN H, ASP 473 TO GLU
Sequence detailsTHE UNIPROT DATABASE ENTRY FOR THIS SEQUENCE (P00877) HAS A VARIANT (LEU46PRO) WHICH OCCURS IN ...THE UNIPROT DATABASE ENTRY FOR THIS SEQUENCE (P00877) HAS A VARIANT (LEU46PRO) WHICH OCCURS IN STRAIN 21GR AND 2137.

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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: 2.44 Å3/Da / Density % sol: 49.28 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0917
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0917 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 125065 / % possible obs: 98.4 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.63 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GK8

1gk8


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 15.453 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VERY WEAK DENSITIES WERE OBSERVED FOR SOME RESIDUE SIDE CHAINS. RESIDUES ARG84, MET87 ARG130, ASN136 AND LYS137 OF THE SMALL SUBUNIT WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VERY WEAK DENSITIES WERE OBSERVED FOR SOME RESIDUE SIDE CHAINS. RESIDUES ARG84, MET87 ARG130, ASN136 AND LYS137 OF THE SMALL SUBUNIT WERE THUS MODELED ON EXISTING HIGH RESOLUTION STRUCTURES AND HAVE HIGH B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 6228 5 %RANDOM
Rwork0.197 ---
obs0.198 118598 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.18 Å20 Å2-2.01 Å2
2---2.54 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37837 0 272 395 38504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02239025
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.95752897
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30554785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09623.1251827
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.682156227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.39215312
X-RAY DIFFRACTIONr_chiral_restr0.0940.25608
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0230080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.219106
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.226696
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.21489
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4220.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.524317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08238257
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.24316754
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0444.514640
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

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3581tight positional00.05
2B3581tight positional0.040.05
3C3581tight positional0.040.05
4D3581tight positional0.040.05
5E3581tight positional0.040.05
6F3581tight positional0.040.05
7G3581tight positional0.040.05
8H3581tight positional0.040.05
9I1143tight positional00.05
10J1143tight positional0.040.05
11K1143tight positional0.040.05
12L1143tight positional0.040.05
13M1143tight positional0.040.05
14N1143tight positional0.040.05
15O1143tight positional0.040.05
16P1143tight positional0.040.05
1A3581tight thermal00.5
2B3581tight thermal0.130.5
3C3581tight thermal0.130.5
4D3581tight thermal0.120.5
5E3581tight thermal0.10.5
6F3581tight thermal0.120.5
7G3581tight thermal0.110.5
8H3581tight thermal0.10.5
9I1143tight thermal00.5
10J1143tight thermal0.090.5
11K1143tight thermal0.080.5
12L1143tight thermal0.110.5
13M1143tight thermal0.080.5
14N1143tight thermal0.070.5
15O1143tight thermal0.070.5
16P1143tight thermal0.070.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 462
Rwork0.324 8556

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