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- PDB-2x86: AGME bound to ADP-B-mannose -

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Basic information

Entry
Database: PDB / ID: 2x86
TitleAGME bound to ADP-B-mannose
ComponentsADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
KeywordsISOMERASE / LIPOPOLYSACCHARIDE BIOSYNTHESIS / CARBOHYDRATE METABOLISM / STRESS RESPONSE
Function / homology
Function and homology information


ADP-glyceromanno-heptose 6-epimerase / ADP-glyceromanno-heptose 6-epimerase activity / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / NADP binding
Similarity search - Function
ADP-L-glycero-D-manno-heptose-6-epimerase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / beta-D-mannopyranose / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / ADP-L-glycero-D-manno-heptose-6-epimerase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKowatz, T. / Morrison, J.P. / Tanner, M.E. / Naismith, J.H.
CitationJournal: Protein Sci. / Year: 2010
Title: The Crystal Structure of the Y140F Mutant of Adp-L-Glycero-D-Manno-Heptose 6-Epimerase Bound to Adp-Beta-D-Mannose Suggests a One Base Mechanism.
Authors: Kowatz, T. / Morrison, J.P. / Tanner, M.E. / Naismith, J.H.
History
DepositionMar 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
B: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
C: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
D: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
E: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
F: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
G: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
H: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
I: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
J: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
K: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
L: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
M: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
N: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
O: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
P: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
Q: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
R: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
S: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
T: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)824,66579
Polymers797,83020
Non-polymers26,83559
Water16,664925
1
A: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
B: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
C: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
D: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
E: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,03119
Polymers199,4585
Non-polymers6,57414
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-27.7 kcal/mol
Surface area67920 Å2
MethodPISA
2
F: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
G: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
H: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
I: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
J: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,21120
Polymers199,4585
Non-polymers6,75415
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-30.4 kcal/mol
Surface area67870 Å2
MethodPISA
3
K: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
L: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
M: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
N: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
O: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,21120
Polymers199,4585
Non-polymers6,75415
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-47.3 kcal/mol
Surface area67770 Å2
MethodPISA
4
P: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
Q: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
R: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
S: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
T: ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,21120
Polymers199,4585
Non-polymers6,75415
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-46.8 kcal/mol
Surface area67820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.074, 162.458, 185.027
Angle α, β, γ (deg.)90.00, 101.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE / AGME / ADP-HEP 6-EPIMERASE / ADP-L-GLYCERO-BETA-D-MANNO-HEPTOSE-6-EPIMERASE / ADP-GLYCEROMANNO- ...AGME / ADP-HEP 6-EPIMERASE / ADP-L-GLYCERO-BETA-D-MANNO-HEPTOSE-6-EPIMERASE / ADP-GLYCEROMANNO-HEPTOSE 6-EPIMERASE


Mass: 39891.512 Da / Num. of mol.: 20 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P67911, ADP-glyceromanno-heptose 6-epimerase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 140 TO PHE ...ENGINEERED RESIDUE IN CHAIN A, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN C, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN E, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN F, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN G, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN H, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN I, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN J, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN K, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN L, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN M, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN N, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN O, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN P, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN Q, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN R, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN S, TYR 140 TO PHE ENGINEERED RESIDUE IN CHAIN T, TYR 140 TO PHE
Sequence detailsHIS TAG AT N-TERMINUS, Y140F MUTATION

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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: 2.55 Å3/Da / Density % sol: 51.75 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU CCD RIGAKU / Detector: CCD / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→33 Å / Num. obs: 197672 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.8 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.6.0060refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQ2

1eq2


Resolution: 2.8→35.05 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.902 / SU B: 32.587 / SU ML: 0.303 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27239 9661 5.1 %RANDOM
Rwork0.2522 ---
obs0.25321 181448 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.715 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.03 Å2
2--0.15 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48800 0 1709 925 51434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02251808
X-RAY DIFFRACTIONr_bond_other_d0.0060.0234053
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.98370363
X-RAY DIFFRACTIONr_angle_other_deg2.399382740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29956120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63924.7292580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.854158160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.51715200
X-RAY DIFFRACTIONr_chiral_restr0.0690.27415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0257768
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0211020
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2.795→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 647 -
Rwork0.467 12604 -
obs--91.68 %
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)
11.4011-0.74380.71832.7238-0.09392.21850.0420.110.06370.1155-0.0175-0.36240.26630.2136-0.02450.1477-0.00610.06380.1950.0140.190423.581-32.11680.306
21.9554-0.13870.94082.9510.47232.9251-0.09290.07520.04790.46860.1287-0.5898-0.03980.5195-0.03580.45990.0389-0.19910.261-0.01270.315142.179-14.62110.598
31.9206-0.76470.2862.8480.18792.3182-0.09390.00650.21650.26520.1493-0.4936-0.25730.3077-0.05540.5936-0.0985-0.07850.1809-0.05250.250631.3923.599110.925
41.3462-0.09820.61012.1805-0.57992.2736-0.00190.03490.13460.1673-0.00720.0489-0.34640.00350.00910.32820.04190.0870.15540.00690.16295.45129.43881.577
51.0461-0.04590.44442.423-0.26961.8331-0.06790.11230.0099-0.0155-0.01090.1527-0.0676-0.02180.07880.0417-0.0180.06480.2422-0.02130.14630.815-5.0262.541
61.1448-0.44590.76782.77140.22952.15450.08620.07930.0222-0.1826-0.0145-0.35570.25930.188-0.07170.1890.00220.11580.18430.00630.1745-18.983-32.121125.036
71.14990.1460.96893.25241.01813.26660.04390.099-0.03870.39510.1503-0.78410.20820.6401-0.19420.23540.0559-0.12240.3211-0.02180.4053-0.873-14.663155.684
81.4022-0.40010.38282.1824-0.07512.0024-0.02730.03640.13360.24630.0209-0.2969-0.29320.33810.00640.2472-0.10620.0480.2284-0.03690.1876-11.8223.605156.018
91.3010.00930.51131.9963-0.38132.03840.0190.03620.1367-0.01170.04190.0518-0.16850.0341-0.06090.10550.03820.11740.18420.00440.1629-37.07129.456126.106
101.2064-0.17550.79232.60020.07291.80640.03030.1218-0.0132-0.299-0.04280.14560.11110.0240.01250.0824-0.00430.0520.2127-0.02440.1302-41.403-4.92106.879
112.0599-0.01981.3932.3505-0.46022.8170.1379-0.16-0.2991-0.08520.1740.25070.1698-0.3939-0.31190.1678-0.0527-0.03480.21870.04150.237616.48967.201115.306
121.33940.64240.40052.3528-0.18451.5655-0.18990.10810.1793-0.28990.16740.0532-0.1948-0.11680.02250.2682-0.0123-0.00240.18370.00930.178133.869102.701111.786
131.20720.14120.78032.34560.24721.9492-0.0645-0.02950.06380.12040.0139-0.1132-0.2050.09680.05060.1002-0.03190.01410.2254-0.0740.277557.353107.976143.142
142.11210.26230.93672.9882-0.49251.94890.1047-0.6904-0.14360.56880.0176-0.14490.0541-0.2482-0.12220.18120.006-0.02770.45290.02710.28155.55875.356165.681
152.01020.42591.65232.75670.03922.55560.5017-0.6564-0.57220.28270.10630.31270.4747-0.7073-0.6080.283-0.1787-0.14070.41820.3070.552530.30150.022148.331
161.6216-0.10390.87882.3498-0.55622.64860.048-0.1846-0.1836-0.05750.09640.30810.013-0.4201-0.14450.05340.00760.05860.24980.00320.1769-26.74567.016160.044
171.51240.60920.41062.0713-0.07182.0064-0.22450.10230.2653-0.15670.1270.0146-0.2644-0.17410.09750.20860.01540.01790.17830.01430.1959-9.219102.463156.782
181.04310.06820.783.77420.0882.0947-0.1068-0.03280.14550.42730.0336-0.3948-0.19080.14740.07330.2465-0.0112-0.12370.2091-0.05490.348612.957108.004188.97
191.23270.45090.38984.4558-1.12331.7464-0.0481-0.35130.08911.5012-0.0113-0.4177-0.2685-0.02150.05930.83050.1087-0.20890.3232-0.04960.231810.16575.542211.705
201.10290.07750.55322.6982-0.07361.9405-0.0447-0.2464-0.1660.41940.21990.39650.084-0.3418-0.17510.21310.0470.14020.34360.13070.2391-14.39450.072193.743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 307
2X-RAY DIFFRACTION2B1 - 307
3X-RAY DIFFRACTION3C1 - 307
4X-RAY DIFFRACTION4D1 - 307
5X-RAY DIFFRACTION5E1 - 307
6X-RAY DIFFRACTION6F1 - 307
7X-RAY DIFFRACTION7G1 - 307
8X-RAY DIFFRACTION8H1 - 307
9X-RAY DIFFRACTION9I1 - 307
10X-RAY DIFFRACTION10J1 - 307
11X-RAY DIFFRACTION11K1 - 307
12X-RAY DIFFRACTION12L1 - 307
13X-RAY DIFFRACTION13M1 - 307
14X-RAY DIFFRACTION14N1 - 307
15X-RAY DIFFRACTION15O1 - 307
16X-RAY DIFFRACTION16P1 - 307
17X-RAY DIFFRACTION17Q1 - 307
18X-RAY DIFFRACTION18R1 - 307
19X-RAY DIFFRACTION19S1 - 307
20X-RAY DIFFRACTION20T1 - 307

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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

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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

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