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- PDB-4mgg: Crystal structure of an enolase (mandelate racemase subgroup) fro... -

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Basic information

Entry
Database: PDB / ID: 4mgg
TitleCrystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121
ComponentsMuconate lactonizing enzyme
KeywordsISOMERASE / Enolase / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / PSI-Biology
Function / homology
Function and homology information


cis-L-3-hydroxyproline dehydratase / alpha-amino acid metabolic process / hydro-lyase activity / amino acid binding / isomerase activity / cellular response to amino acid stimulus / magnesium ion binding
Similarity search - Function
cis-3-Hydroxy-L-proline dehydratase / 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 ...cis-3-Hydroxy-L-proline dehydratase / 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
NICKEL (II) ION / Cis-3-hydroxy-L-proline dehydratase
Similarity search - Component
Biological speciesLabrenzia aggregata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVetting, M.W. / Zhang, X. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121
Authors: Vetting, M.W. / Zhang, X. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...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: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Muconate lactonizing enzyme
B: Muconate lactonizing enzyme
C: Muconate lactonizing enzyme
D: Muconate lactonizing enzyme
E: Muconate lactonizing enzyme
F: Muconate lactonizing enzyme
G: Muconate lactonizing enzyme
H: Muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,91431
Polymers319,2188
Non-polymers69623
Water33,8321878
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23540 Å2
ΔGint-260 kcal/mol
Surface area89410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.313, 154.897, 181.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is an octamer

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Components

#1: Protein
Muconate lactonizing enzyme


Mass: 39902.246 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Labrenzia aggregata (bacteria) / Strain: IAM 12614 / Gene: SIAM614_28497 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0NXQ8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1878 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (17 mb\g/ml, 5mM Mg2+, 20mM Tris buffer (pH=7.9), 5% glycerol); Reservoir (40 % w/v pentaerythritol propoxylate (17/8 PO/OH) 0.2 M magnesium chloride 5.5 0.1 M MES-NaOH (MIDAS F8)); ...Details: Protein (17 mb\g/ml, 5mM Mg2+, 20mM Tris buffer (pH=7.9), 5% glycerol); Reservoir (40 % w/v pentaerythritol propoxylate (17/8 PO/OH) 0.2 M magnesium chloride 5.5 0.1 M MES-NaOH (MIDAS F8)); Cryoprotection (Reservoir), pH 6.5, sitting drop, vapor diffuction, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 28, 2013 / 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: 2.2→181.983 Å / Num. all: 158072 / Num. obs: 158072 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 23.44 Å2 / Rmerge(I) obs: 0.184 / Rsym value: 0.184 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.327.10.8040.9163100228270.80499.8
2.32-2.467.20.6041.3156299216560.60499.9
2.46-2.637.30.4571.7148074203770.457100
2.63-2.847.40.2962.5139776189990.296100
2.84-3.117.50.2063.7131174175160.206100
3.11-3.487.50.1484.6119290159180.148100
3.48-4.027.40.1284.9104418141030.128100
4.02-4.927.30.1095.687251119860.109100
4.92-6.967.40.0826.96913893810.082100
6.96-40.80970.042153728853090.04299.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PMQ
Resolution: 2.2→40.809 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8554 / SU ML: 0.24 / σ(F): 0 / σ(I): 0 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 7926 5.02 %RANDOM
Rwork0.1503 ---
all0.1536 157964 --
obs0.1536 157964 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.13 Å2 / Biso mean: 29.9691 Å2 / Biso min: 6.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21977 0 23 1878 23878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01422511
X-RAY DIFFRACTIONf_angle_d1.38430728
X-RAY DIFFRACTIONf_chiral_restr0.0793510
X-RAY DIFFRACTIONf_plane_restr0.0073963
X-RAY DIFFRACTIONf_dihedral_angle_d14.0728185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.30122830.21384890517399
2.225-2.25120.31992830.232149795262100
2.2512-2.27860.29392910.221548575148100
2.2786-2.30750.29032770.191749595236100
2.3075-2.33780.25412400.178849385178100
2.3378-2.36980.26052710.177449625233100
2.3698-2.40370.26022680.176349375205100
2.4037-2.43960.26952480.171549725220100
2.4396-2.47770.25282600.171949325192100
2.4777-2.51830.26712670.175749715238100
2.5183-2.56170.26112680.174149895257100
2.5617-2.60830.23382710.161949335204100
2.6083-2.65850.2382490.151449985247100
2.6585-2.71270.22642680.151149825250100
2.7127-2.77170.22992650.152549675232100
2.7717-2.83610.22362600.155550195279100
2.8361-2.9070.22372380.151949985236100
2.907-2.98560.23652590.152749985257100
2.9856-3.07340.21272510.157149965247100
3.0734-3.17260.2442640.150849895253100
3.1726-3.2860.22792740.152450045278100
3.286-3.41750.20392510.149850035254100
3.4175-3.57290.19662360.146750645300100
3.5729-3.76120.1942620.145850085270100
3.7612-3.99660.20052760.130950135289100
3.9966-4.30490.15582410.118850895330100
4.3049-4.73750.18022520.107750845336100
4.7375-5.42170.15842860.116750775363100
5.4217-6.82560.20682980.138551245422100
6.8256-40.81610.16012690.14785306557599
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)
10.47810.0604-0.1330.7834-0.03220.28270.0129-0.1694-0.23780.0051-0.01820.08540.0419-0.02690.01130.0876-0.03440.00520.13550.01470.2133-33.0791-39.90616.5528
21.0959-0.08960.0160.91390.0531.28590.0155-0.10730.00410.1762-0.04150.0701-0.03510.0457-0.00040.0781-0.03490.01120.10880.00240.1744-39.3707-29.01746.5274
30.6152-0.13850.21250.3475-0.04630.22830.00670.0317-0.00690.0199-0.0309-0.0270.04780.01880.01710.07540.00370.01610.11810.00130.1468-13.3923-30.51292.37
40.4476-0.03090.04280.5857-0.05220.62390.05350.0185-0.1581-0.0846-0.04890.04760.1004-0.00670.0080.0654-0.0078-0.00890.1223-0.02570.175-30.9735-37.4246-5.2859
50.5194-0.22140.18710.83830.47960.9773-0.01590.09010.0959-0.1099-0.0862-0.0835-0.0880.0970.06010.23540.0209-0.05410.20420.04190.1455-34.79637.5005-19.7071
60.6013-0.3914-0.08111.3014-0.12830.87510.10550.10990.0028-0.3036-0.1297-0.0882-0.06430.10640.01190.15830.0347-0.00310.18410.02730.0954-31.2472-7.9212-22.0468
70.6480.18150.27250.47860.24020.5162-0.03680.00380.1060.02680.00270.0297-0.1381-0.03060.02660.12390.0107-0.00810.10310.01410.1192-30.31647.2990.4387
80.38040.01540.09120.6573-0.1870.7308-0.00970.04520.002-0.1085-0.03910.1787-0.1255-0.09620.01810.09210.0125-0.03680.13020.00080.1175-43.1802-0.7531-13.2959
90.9441-0.2884-0.02270.7015-0.17630.7228-0.1211-0.0756-0.19230.22250.0356-0.08290.12490.25450.01950.36090.0418-0.05620.2891-0.00530.14848.29583.602654.6196
101.0939-0.0536-0.25980.167-0.2370.743-0.1491-0.1321-0.04710.17090.0897-0.13110.01030.3960.05230.1987-0.0025-0.06230.347-0.00210.196418.86765.917742.9097
110.42920.2802-0.02890.61340.05680.73790.0004-0.03720.01220.0902-0.04010.0235-0.11830.0090.03170.17990.0004-0.01810.1035-0.01320.101-5.295312.097337.6383
120.5893-0.0472-0.41680.5972-0.00470.3221-0.0307-0.27240.130.18310.0352-0.168-0.1620.3693-0.01010.3319-0.0651-0.09830.3274-0.02480.179311.239616.544750.626
131.01950.21570.62751.38690.09140.88920.0042-0.00090.17690.0594-0.0129-0.2657-0.26240.26120.03760.3432-0.14920.04040.26470.0570.311517.263828.037-3.6369
140.4434-0.0557-0.05040.1561-0.39411.19-0.0072-0.00110.16880.0737-0.0911-0.0796-0.76880.06070.03410.3964-0.034-0.03320.15180.01770.1723-5.40725.49629.4845
150.9663-0.0820.28880.65250.15270.60430.08360.0180.2568-0.196-0.1054-0.087-0.36150.10720.00220.3531-0.08740.02710.1770.0460.24284.446531.1625-5.9925
160.3674-0.050.3290.2867-0.01060.2819-0.2551-0.20870.2350.39530.1017-0.2471-0.1589-0.0741-0.08440.45670.1586-0.21740.3421-0.04670.27589.1279-26.995448.609
171.0392-0.13370.28770.2747-0.29420.44940.0076-0.193-0.00880.16830.0366-0.0236-0.112-0.15340.10610.61660.2923-0.26130.2975-0.00270.12360.7474-26.569854.0327
180.8038-0.1779-0.09850.56760.17870.6204-0.282-0.28670.18940.35290.2438-0.1206-0.03480.01310.05710.40760.148-0.09030.2391-0.03340.1874-6.7172-22.3149.1671
190.70250.1231-0.16290.8389-0.32960.7299-0.0303-0.0295-0.0560.0049-0.0554-0.17290.21340.29430.01830.17730.0815-0.02680.18850.03620.250814.9999-34.638426.6479
200.92790.20580.1130.5559-0.03470.3883-0.0213-0.01270.12620.1111-0.0507-0.0085-0.14820.08590.04250.1350.0108-0.03420.12430.02290.15976.8787-18.661122.9298
210.0684-0.1026-0.08250.2964-0.23260.7272-0.1556-0.05560.10540.20470.0828-0.0125-0.0823-0.04220.03570.27610.0604-0.06050.13650.01450.1709-3.7221-25.872835.2366
220.7133-0.0995-0.13750.2691-0.13780.26-0.3063-0.2118-0.03280.37210.1917-0.01590.20330.0337-0.05120.43660.1556-0.10550.24760.030.13030.6238-35.81946.0569
230.4467-0.1272-0.15960.27590.40030.91580.06590.0718-0.0699-0.1244-0.24490.0774-0.1558-0.05020.06010.43330.076-0.09480.3731-0.02360.2403-3.5783-2.9549-31.6379
240.8443-0.26510.11111.38440.67810.84730.0540.0114-0.0344-0.3324-0.14940.1602-0.2507-0.15330.01710.39040.1063-0.08030.29330.00340.1889-8.194310.3077-27.9532
250.3404-0.0924-0.12431.0916-0.13210.69250.03020.1226-0.0821-0.2419-0.0802-0.1007-0.00190.04520.03730.1240.0110.00870.20760.02260.16195.261-4.8927-18.6749
261.11410.00760.39380.84390.41070.9361-0.127-0.04-0.1580.22630.1020.16530.2109-0.10130.01270.2518-0.00540.07570.17310.05920.1947-32.778-29.124535.9353
272.3821-0.49560.43251.37290.22152.075-0.04140.18220.26550.0310.02590.38-0.4699-0.50210.01050.29590.13590.05710.38020.06070.3243-43.93523.163438.5862
280.5782-0.1478-0.28390.8426-0.04250.6074-0.1334-0.0696-0.0240.14530.14220.11470.0131-0.169-0.01910.17570.01660.02430.17480.01430.1257-31.0061-9.040732.8076
290.8449-0.1425-0.03220.8986-0.2680.66640.0425-0.00570.0533-0.24490.0351-0.2415-0.36140.2980.00090.2047-0.2141-0.00480.4227-0.00350.391131.118817.079217.7525
300.77030.09370.42580.7030.27520.5703-0.03080.1128-0.1138-0.07850.0869-0.22780.00130.4074-0.05520.1121-0.0324-0.01470.34180.02060.287327.3544-2.525514.9605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 40 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 117 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 297 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 367 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 29 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 117 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 118 through 297 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 298 through 367 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 75 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 76 through 135 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 136 through 309 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 310 through 367 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 0 through 117 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 118 through 271 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 272 through 367 )D0
16X-RAY DIFFRACTION16chain 'E' and (resid 0 through 29 )E0
17X-RAY DIFFRACTION17chain 'E' and (resid 30 through 61 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 62 through 135 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 136 through 193 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 194 through 255 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 256 through 310 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 311 through 367 )E0
23X-RAY DIFFRACTION23chain 'F' and (resid 0 through 29 )F0
24X-RAY DIFFRACTION24chain 'F' and (resid 30 through 98 )F0
25X-RAY DIFFRACTION25chain 'F' and (resid 99 through 367 )F0
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 134 )G0
27X-RAY DIFFRACTION27chain 'G' and (resid 135 through 156 )G0
28X-RAY DIFFRACTION28chain 'G' and (resid 157 through 367 )G0
29X-RAY DIFFRACTION29chain 'H' and (resid 0 through 117 )H0
30X-RAY DIFFRACTION30chain 'H' and (resid 118 through 367 )H0

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