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- PDB-2xf8: Structure of the D-Erythrose-4-Phosphate Dehydrogenase from E. co... -

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Basic information

Entry
Database: PDB / ID: 2xf8
TitleStructure of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli in complex with a NAD cofactor analog (3-Chloroacetyl adenine pyridine dinucleotide) and sulfate anion
ComponentsD-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / HYDRIDE TRANSFER / COFACTOR ANALOG / PYRIDOXAL PHOPHATE BIOSYNTHESIS
Function / homology
Function and homology information


erythrose-4-phosphate dehydrogenase / erythrose-4-phosphate dehydrogenase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / cytosol
Similarity search - Function
D-erythrose-4-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...D-erythrose-4-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(CHLOROACETYL) PYRIDINE ADENINE DINUCLEOTIDE / D-erythrose-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMoniot, S. / Didierjean, C. / Boschi-Muller, S. / Branlant, G. / Corbier, C.
CitationJournal: To be Published
Title: Structural Characterization of Erythrose-4- Phosphate Dehydrogenase from Escherichia Coli: Peculiar Features When Compared to Phosphorylating Gapdhs
Authors: Moniot, S. / Didierjean, C. / Boschi-Muller, S. / Branlant, G. / Corbier, C.
History
DepositionMay 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
B: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
C: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
D: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
E: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
F: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
G: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
H: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
I: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
J: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
K: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
L: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
M: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
N: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
O: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
P: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)602,57840
Polymers595,45816
Non-polymers7,12024
Water3,081171
1
E: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
F: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
G: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
H: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,64510
Polymers148,8654
Non-polymers1,7806
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12980 Å2
ΔGint-141 kcal/mol
Surface area44820 Å2
MethodPISA
2
A: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
B: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
C: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
D: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,64510
Polymers148,8654
Non-polymers1,7806
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-137.4 kcal/mol
Surface area45120 Å2
MethodPISA
3
M: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
N: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
O: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
P: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,64510
Polymers148,8654
Non-polymers1,7806
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-138.6 kcal/mol
Surface area45460 Å2
MethodPISA
4
I: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
J: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
K: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
L: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,64510
Polymers148,8654
Non-polymers1,7806
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-140 kcal/mol
Surface area45790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.180, 111.660, 135.470
Angle α, β, γ (deg.)91.30, 96.11, 88.44
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 21
2112B1 - 21
3112C1 - 21
4112D1 - 21
5112E1 - 21
6112F1 - 21
7112G1 - 21
8112H1 - 21
9112I1 - 21
10112J1 - 21
11112K1 - 21
12112L1 - 21
13112M1 - 21
14112N1 - 21
15112O1 - 21
16112P1 - 21
1212A27 - 30
2212B27 - 30
3212C27 - 30
4212D27 - 30
5212E27 - 30
6212F27 - 30
7212G27 - 30
8212H27 - 30
9212I27 - 30
10212J27 - 30
11212K27 - 30
12212L27 - 30
13212M27 - 30
14212N27 - 30
15212O27 - 30
16212P27 - 30
1312A41 - 46
2312B41 - 46
3312C41 - 46
4312D41 - 46
5312E41 - 46
6312F41 - 46
7312G41 - 46
8312H41 - 46
9312I41 - 46
10312J41 - 46
11312K41 - 46
12312L41 - 46
13312M41 - 46
14312N41 - 46
15312O41 - 46
16312P41 - 46
1412A52 - 57
2412B52 - 57
3412C52 - 57
4412D52 - 57
5412E52 - 57
6412F52 - 57
7412G52 - 57
8412H52 - 57
9412I52 - 57
10412J52 - 57
11412K52 - 57
12412L52 - 57
13412M52 - 57
14412N52 - 57
15412O52 - 57
16412P52 - 57
1512A73 - 75
2512B73 - 75
3512C73 - 75
4512D73 - 75
5512E73 - 75
6512F73 - 75
7512G73 - 75
8512H73 - 75
9512I73 - 75
10512J73 - 75
11512K73 - 75
12512L73 - 75
13512M73 - 75
14512N73 - 75
15512O73 - 75
16512P73 - 75
1612A81 - 100
2612B81 - 100
3612C81 - 100
4612D81 - 100
5612E81 - 100
6612F81 - 100
7612G81 - 100
8612H81 - 100
9612I81 - 100
10612J81 - 100
11612K81 - 100
12612L81 - 100
13612M81 - 100
14612N81 - 100
15612O81 - 100
16612P81 - 100
1712A103 - 120
2712B103 - 120
3712C103 - 120
4712D103 - 120
5712E103 - 120
6712F103 - 120
7712G103 - 120
8712H103 - 120
9712I103 - 120
10712J103 - 120
11712K103 - 120
12712L103 - 120
13712M103 - 120
14712N103 - 120
15712O103 - 120
16712P103 - 120
1812A128 - 136
2812B128 - 136
3812C128 - 136
4812D128 - 136
5812E128 - 136
6812F128 - 136
7812G128 - 136
8812H128 - 136
9812I128 - 136
10812J128 - 136
11812K128 - 136
12812L128 - 136
13812M128 - 136
14812N128 - 136
15812O128 - 136
16812P128 - 136
1912A142 - 182
2912B142 - 182
3912C142 - 182
4912D142 - 182
5912E142 - 182
6912F142 - 182
7912G142 - 182
8912H142 - 182
9912I142 - 182
10912J142 - 182
11912K142 - 182
12912L142 - 182
13912M142 - 182
14912N142 - 182
15912O142 - 182
16912P142 - 182
11012A213 - 263
21012B213 - 263
31012C213 - 263
41012D213 - 263
51012E213 - 263
61012F213 - 263
71012G213 - 263
81012H213 - 263
91012I213 - 263
101012J213 - 263
111012K213 - 263
121012L213 - 263
131012M213 - 263
141012N213 - 263
151012O213 - 263
161012P213 - 263
11112A265 - 330
21112B265 - 330
31112C265 - 330
41112D265 - 330
51112E265 - 330
61112F265 - 330
71112G265 - 330
81112H265 - 330
91112I265 - 330
101112J265 - 330
111112K265 - 330
121112L265 - 330
131112M265 - 330
141112N265 - 330
151112O265 - 330
161112P265 - 330

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Components

#1: Protein
D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE / E4PDH


Mass: 37216.133 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE IN COVALENT COMPLEX WITH A COFACTOR ANALOG THROUGH ITS CATALYTIC CYSTEINE (C149)
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Variant: TG1 / Plasmid: PBLUESCRIPT(SK) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): HB101
References: UniProt: P0A9B6, erythrose-4-phosphate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-3CD / 3-(CHLOROACETYL) PYRIDINE ADENINE DINUCLEOTIDE / 3-CAPAD


Mass: 697.890 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H28ClN6O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3-(CHLOROACETYL)PYRIDINE ADENINE DINUCLEOTIDE (3CD): COVALENTLY BOND TO THE CATALYTIC CYSTEINE C149

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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: 2.57 Å3/Da / Density % sol: 51.7 % / Description: NONE
Crystal growpH: 8.5
Details: 20 % (W/V) PEG 2000 MME, 100 MM TRIS-HCL BUFFER PH 8.5, 200 MM LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.95→48.7 Å / Num. obs: 112592 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.1
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X5J
Resolution: 2.95→48.72 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.868 / SU B: 25.079 / SU ML: 0.452 / Cross valid method: THROUGHOUT / ESU R Free: 0.515 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27981 5630 5 %RANDOM
Rwork0.23688 ---
obs0.23904 106962 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.162 Å2
Baniso -1Baniso -2Baniso -3
1-4.95 Å2-2.66 Å2-2.68 Å2
2---2.48 Å2-0.83 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39641 0 432 171 40244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02140811
X-RAY DIFFRACTIONr_bond_other_d0.0090.0226556
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.94855596
X-RAY DIFFRACTIONr_angle_other_deg1.825364526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10955120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63923.4131846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.744156496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.06415341
X-RAY DIFFRACTIONr_chiral_restr0.0630.26556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0245614
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028427
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_it0.4711.525543
X-RAY DIFFRACTIONr_mcbond_other0.0591.510492
X-RAY DIFFRACTIONr_mcangle_it0.906241217
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.087315268
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9954.514379
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1422tight positional0.030.05
2B1422tight positional0.040.05
3C1422tight positional0.030.05
4D1422tight positional0.030.05
5E1422tight positional0.040.05
6F1422tight positional0.030.05
7G1422tight positional0.030.05
8H1422tight positional0.030.05
9I1422tight positional0.030.05
10J1422tight positional0.030.05
11K1422tight positional0.030.05
12L1422tight positional0.030.05
13M1422tight positional0.030.05
14N1422tight positional0.030.05
15O1422tight positional0.030.05
16P1422tight positional0.030.05
1A1645medium positional0.090.5
2B1645medium positional0.140.5
3C1645medium positional0.090.5
4D1645medium positional0.160.5
5E1645medium positional0.140.5
6F1645medium positional0.150.5
7G1645medium positional0.110.5
8H1645medium positional0.10.5
9I1645medium positional0.090.5
10J1645medium positional0.110.5
11K1645medium positional0.110.5
12L1645medium positional0.120.5
13M1645medium positional0.150.5
14N1645medium positional0.10.5
15O1645medium positional0.090.5
16P1645medium positional0.120.5
1A1422tight thermal0.060.5
2B1422tight thermal0.060.5
3C1422tight thermal0.060.5
4D1422tight thermal0.070.5
5E1422tight thermal0.070.5
6F1422tight thermal0.060.5
7G1422tight thermal0.060.5
8H1422tight thermal0.050.5
9I1422tight thermal0.070.5
10J1422tight thermal0.060.5
11K1422tight thermal0.070.5
12L1422tight thermal0.070.5
13M1422tight thermal0.050.5
14N1422tight thermal0.070.5
15O1422tight thermal0.090.5
16P1422tight thermal0.060.5
1A1645medium thermal0.052
2B1645medium thermal0.052
3C1645medium thermal0.052
4D1645medium thermal0.052
5E1645medium thermal0.052
6F1645medium thermal0.052
7G1645medium thermal0.052
8H1645medium thermal0.052
9I1645medium thermal0.052
10J1645medium thermal0.052
11K1645medium thermal0.052
12L1645medium thermal0.062
13M1645medium thermal0.052
14N1645medium thermal0.052
15O1645medium thermal0.062
16P1645medium thermal0.052
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 419 -
Rwork0.331 7954 -
obs--100 %

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