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- PDB-4h2h: Crystal structure of an enolase (mandalate racemase subgroup, tar... -

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Basic information

Entry
Database: PDB / ID: 4h2h
TitleCrystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine)
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsISOMERASE / Enolase / mandelate racemase subgroup / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


4-hydroxyproline betaine 2-epimerase / amino-acid betaine catabolic process / racemase activity, acting on amino acids and derivatives / racemase and epimerase activity, acting on amino acids and derivatives / magnesium ion binding
Similarity search - Function
4R-hydroxyproline betaine 2-epimerase / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain ...4R-hydroxyproline betaine 2-epimerase / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0XW / IODIDE ION / NICKEL (II) ION / 4-hydroxyproline betaine 2-epimerase
Similarity search - Component
Biological speciesPelagibaca bermudensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVetting, M.W. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Nature / Year: 2013
Title: Discovery of new enzymes and metabolic pathways by using structure and genome context.
Authors: Zhao, S. / Kumar, R. / Sakai, A. / Vetting, M.W. / Wood, B.M. / Brown, S. / Bonanno, J.B. / Hillerich, B.S. / Seidel, R.D. / Babbitt, P.C. / Almo, S.C. / Sweedler, J.V. / Gerlt, J.A. / ...Authors: Zhao, S. / Kumar, R. / Sakai, A. / Vetting, M.W. / Wood, B.M. / Brown, S. / Bonanno, J.B. / Hillerich, B.S. / Seidel, R.D. / Babbitt, P.C. / Almo, S.C. / Sweedler, J.V. / Gerlt, J.A. / Cronan, J.E. / Jacobson, M.P.
History
DepositionSep 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _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: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
G: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,29090
Polymers325,6098
Non-polymers9,68182
Water37,2192066
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29200 Å2
ΔGint-147 kcal/mol
Surface area80820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.035, 152.824, 113.027
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Mandelate racemase/muconate lactonizing enzyme


Mass: 40701.141 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelagibaca bermudensis (bacteria) / Strain: HTCC2601 / Gene: R2601_01638 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0FPQ4

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Non-polymers , 6 types, 2148 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-0XW / (2S,4R)-4-hydroxy-1,1-dimethylpyrrolidinium-2-carboxylate / Betonicine / L-4-Hydroxyproline betaine


Mass: 159.183 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H13NO3
#5: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 61 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2066 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 10% glycerol, 50 mM MgCl2, 5 mM EDTA, 2 mM NiCl2; Reservoir (0.1 M HEPES:NaOH pH 7.5 70% (v/v) MPD); Soak 2 minutes in (Reservoir + 50 mM MgCl2, 200 ...Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 10% glycerol, 50 mM MgCl2, 5 mM EDTA, 2 mM NiCl2; Reservoir (0.1 M HEPES:NaOH pH 7.5 70% (v/v) MPD); Soak 2 minutes in (Reservoir + 50 mM MgCl2, 200 mM 4-OH Proline Betaine ) Cryoprotection (Soaking solution), sitting drop vapor diffuction, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 14, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→109.072 Å / Num. obs: 325934 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.085 / Net I/σ(I): 8.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.577 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PMQ
Resolution: 1.7→25.68 Å / Occupancy max: 1 / Occupancy min: 0.11 / SU ML: 0.17 / σ(F): 0 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 16434 5.04 %
Rwork0.159 --
obs0.16 325787 99.9 %
all-325787 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22160 0 183 2066 24409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123114
X-RAY DIFFRACTIONf_angle_d1.10931597
X-RAY DIFFRACTIONf_dihedral_angle_d12.8028323
X-RAY DIFFRACTIONf_chiral_restr0.0743501
X-RAY DIFFRACTIONf_plane_restr0.0064139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.26835220.235910371X-RAY DIFFRACTION100
1.7193-1.73950.2695680.236210272X-RAY DIFFRACTION100
1.7395-1.76070.25915350.226310326X-RAY DIFFRACTION100
1.7607-1.7830.25835590.227210190X-RAY DIFFRACTION100
1.783-1.80650.25815730.22110257X-RAY DIFFRACTION100
1.8065-1.83120.23875580.205910341X-RAY DIFFRACTION100
1.8312-1.85740.23945620.195810284X-RAY DIFFRACTION100
1.8574-1.88510.21865410.184810284X-RAY DIFFRACTION100
1.8851-1.91450.21035400.173710309X-RAY DIFFRACTION100
1.9145-1.94590.21865550.178510285X-RAY DIFFRACTION100
1.9459-1.97950.22185280.175810380X-RAY DIFFRACTION100
1.9795-2.01540.21275640.169110250X-RAY DIFFRACTION100
2.0154-2.05420.20545320.160810289X-RAY DIFFRACTION100
2.0542-2.09610.18865290.150210303X-RAY DIFFRACTION100
2.0961-2.14170.19955110.15410363X-RAY DIFFRACTION100
2.1417-2.19150.1955460.15310272X-RAY DIFFRACTION100
2.1915-2.24620.19835690.156510313X-RAY DIFFRACTION100
2.2462-2.30690.1935440.148810304X-RAY DIFFRACTION100
2.3069-2.37480.18675260.152710359X-RAY DIFFRACTION100
2.3748-2.45140.18875300.156810325X-RAY DIFFRACTION100
2.4514-2.53890.19345450.15910338X-RAY DIFFRACTION100
2.5389-2.64040.19045820.155110264X-RAY DIFFRACTION100
2.6404-2.76050.19615390.16510372X-RAY DIFFRACTION100
2.7605-2.90580.1915630.160310300X-RAY DIFFRACTION100
2.9058-3.08760.20335620.157610309X-RAY DIFFRACTION100
3.0876-3.32560.16485780.142310310X-RAY DIFFRACTION100
3.3256-3.65940.17075280.137810393X-RAY DIFFRACTION100
3.6594-4.18690.14765350.125710373X-RAY DIFFRACTION100
4.1869-5.26760.16165210.134710408X-RAY DIFFRACTION100
5.2676-25.68470.19745890.173710209X-RAY DIFFRACTION98
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)
11.36040.315-1.11711.6159-0.4710.9644-0.1475-0.0244-0.1777-0.0104-0.0064-0.04450.15680.04540.10670.12640.00150.03520.0879-0.01560.130325.8192-38.817116.2366
20.7137-0.3124-0.60320.4020.48470.7656-0.2398-0.3751-0.04620.24490.1912-0.18330.3840.43860.0060.17060.1103-0.04420.27740.00580.19141.7471-21.31236.4527
30.65640.0084-0.27240.83490.25060.6158-0.0746-0.0077-0.1066-0.00290.0074-0.06580.130.05890.04430.09680.01240.01710.08390.00650.112332.5226-26.741520.7017
41.538-0.3271-1.00731.65860.32890.8344-0.13540.0733-0.1798-0.00430.00830.00950.1417-0.08710.08710.1225-0.00880.02880.10010.00970.11694.8534-39.354837.3671
50.71380.251-0.59650.4902-0.58540.9039-0.27080.3279-0.0914-0.32860.26150.21240.4654-0.4524-0.05420.1635-0.1293-0.05350.30810.00870.1961-11.2109-21.397717.5201
60.6577-0.0316-0.22110.8585-0.34270.6106-0.06680.0141-0.09510.00750.03070.05420.0993-0.09380.03390.0856-0.01840.01320.1101-0.00780.0971-2.2448-26.818133.0374
70.71380.5455-0.54281.85940.67961.4370.01940.05010.0296-0.16480.0623-0.3053-0.08740.0004-0.03750.1534-0.03210.03230.12070.04040.188337.219814.9181-4.8728
80.57760.1811-0.30381.2118-0.17410.5481-0.0032-0.07440.0443-0.0488-0.04-0.1899-0.00480.20070.02570.0741-0.0149-0.01560.16580.00650.155346.273.58321.9966
90.42740.2229-0.26840.6123-0.06571.03730.00830.01410.101-0.12980.0434-0.1721-0.11870.0708-0.03980.142-0.0350.03320.10560.0170.189139.44216.66777.1621
100.90060.6926-0.39352.10080.09561.4128-0.03290.13820.0499-0.3122-0.00720.0189-0.008-0.0610.02040.1466-0.01310.0110.1244-0.01190.080429.8637-13.5127-9.3962
110.2503-0.0947-0.15411.20730.50030.25290.17740.36270.087-0.616-0.18320.1255-0.2381-0.37310.05490.20890.0612-0.14040.4084-0.0410.08130.7643-3.6641-4.685
120.5782-0.1701-0.26870.78490.25610.64150.01430.1446-0.0312-0.1951-0.02250.02930.0208-0.11070.01590.1442-0.0216-0.01730.1501-0.00890.088916.8635-13.0353-2.4466
130.9271-0.8008-0.31621.76850.2581.0918-0.0829-0.09190.0170.3330.04780.03580.0613-0.06360.02510.1820.03270.01390.12370.01570.0795-1.6157-16.640363.1647
140.17090.1438-0.0950.8264-0.40850.38630.0646-0.1979-0.02960.4672-0.1186-0.2212-0.11890.26260.01950.2589-0.0111-0.10790.28770.00320.163129.7166-4.502559.1569
150.50170.2731-0.31510.7682-0.24160.5309-0.0039-0.1205-0.00740.21850.0194-0.05060.02010.0772-0.00820.18150.0417-0.03410.1522-0.00050.099713.3284-14.23257.0522
160.9016-0.5977-0.58662.189-0.65331.4089-0.0359-0.0519-0.03470.13480.0670.28110.004-0.0446-0.01490.15370.04250.0050.127-0.03770.1518-6.904113.646360.304
170.4521-0.2983-0.15961.40350.14640.5669-0.02190.02490.01890.0759-0.0230.18570.0104-0.18630.03250.07630.0158-0.01280.1776-0.01360.1427-15.87483.137933.0452
180.4155-0.2529-0.1690.72760.07511.0607-0.023-0.02150.06790.13840.03870.1238-0.0761-0.0798-0.02050.13220.0410.01160.121-0.02280.1656-9.048315.778748.2914
190.1268-0.1209-0.18250.7720.25641.26110.26730.02780.3852-0.0643-0.0209-0.0158-0.485-0.149-0.08950.36480.06870.13770.11990.11160.318117.974639.445313.6029
200.51830.1468-0.51480.58260.03120.49460.12480.29520.1935-0.0872-0.00740.091-0.1901-0.2204-0.04290.15740.0781-0.01320.22670.0720.16782.448221.082812.7064
210.1290.0001-0.09030.0049-0.01210.11130.25380.39980.519-0.15030.03940.1832-0.5942-0.35290.090.45820.30550.06690.1230.38120.249610.511139.3853.2941
220.3792-0.0482-0.17410.975-0.13211.61660.1353-0.06210.3080.01370.0152-0.105-0.40220.0964-0.11560.2846-0.01560.0590.1277-0.05490.259212.300138.877242.748
230.6633-0.3178-0.34130.61830.10450.7090.0801-0.22180.22670.07590.0281-0.1401-0.20990.1591-0.03880.1765-0.0617-0.02390.1834-0.07840.192125.879324.920645.3538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:129)
2X-RAY DIFFRACTION2chain 'A' and (resseq 130:209)
3X-RAY DIFFRACTION3chain 'A' and (resseq 210:367)
4X-RAY DIFFRACTION4chain 'B' and (resseq 2:129)
5X-RAY DIFFRACTION5chain 'B' and (resseq 130:208)
6X-RAY DIFFRACTION6chain 'B' and (resseq 209:367)
7X-RAY DIFFRACTION7chain 'C' and (resseq 2:129)
8X-RAY DIFFRACTION8chain 'C' and (resseq 130:233)
9X-RAY DIFFRACTION9chain 'C' and (resseq 234:367)
10X-RAY DIFFRACTION10chain 'D' and (resseq 2:129)
11X-RAY DIFFRACTION11chain 'D' and (resseq 130:209)
12X-RAY DIFFRACTION12chain 'D' and (resseq 210:367)
13X-RAY DIFFRACTION13chain 'E' and (resseq 2:129)
14X-RAY DIFFRACTION14chain 'E' and (resseq 130:210)
15X-RAY DIFFRACTION15chain 'E' and (resseq 211:367)
16X-RAY DIFFRACTION16chain 'F' and (resseq 2:129)
17X-RAY DIFFRACTION17chain 'F' and (resseq 130:233)
18X-RAY DIFFRACTION18chain 'F' and (resseq 234:367)
19X-RAY DIFFRACTION19chain 'G' and (resseq 2:129)
20X-RAY DIFFRACTION20chain 'G' and (resseq 130:310)
21X-RAY DIFFRACTION21chain 'G' and (resseq 311:367)
22X-RAY DIFFRACTION22chain 'H' and (resseq 2:129)
23X-RAY DIFFRACTION23chain 'H' and (resseq 130:367)

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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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