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- PDB-6cn1: 2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosa... -

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Basic information

Entry
Database: PDB / ID: 6cn1
Title2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Pseudomonas putida in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm
Similarity search - Function
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
(2R)-2-(phosphonooxy)propanoic acid / Chem-EPU / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Pseudomonas putida in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric ...Title: 2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Pseudomonas putida in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
E: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
F: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
G: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
H: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,52137
Polymers362,3708
Non-polymers7,15129
Water5,296294
1
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,74318
Polymers181,1854
Non-polymers3,55814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15660 Å2
ΔGint-90 kcal/mol
Surface area53590 Å2
MethodPISA
2
E: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
F: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
G: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
H: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,77819
Polymers181,1854
Non-polymers3,59315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15660 Å2
ΔGint-100 kcal/mol
Surface area53570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.615, 148.119, 164.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / / Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT


Mass: 45296.191 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: murA, PP_0964 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q88P88, UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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Non-polymers , 5 types, 323 molecules

#2: Chemical
ChemComp-EPU / URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID / ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 677.400 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H29N3O19P2
#3: Chemical
ChemComp-0V5 / (2R)-2-(phosphonooxy)propanoic acid


Mass: 170.058 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.05 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein: 1.4 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3, Screen: PACT (B10), 0.2M Magnesium chloride, 0.1M MES buffer pH 6.0, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 82344 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.058 / Rrim(I) all: 0.148 / Rsym value: 0.136 / Χ2: 1.015 / Net I/σ(I): 13
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3999 / CC1/2: 0.714 / Rpim(I) all: 0.342 / Rrim(I) all: 0.863 / Rsym value: 0.791 / Χ2: 1.002 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BQ2
Resolution: 2.75→29.95 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.897 / SU B: 38.7 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25179 4127 5.1 %RANDOM
Rwork0.20951 ---
obs0.21167 77560 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.033 Å2
Baniso -1Baniso -2Baniso -3
1--2.78 Å20 Å20 Å2
2---0.17 Å20 Å2
3---2.94 Å2
Refinement stepCycle: 1 / Resolution: 2.75→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25218 0 437 294 25949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01926094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0225327
X-RAY DIFFRACTIONr_angle_refined_deg1.2022.00235367
X-RAY DIFFRACTIONr_angle_other_deg0.869358499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.65753364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.15223.9861001
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.993154467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.20915193
X-RAY DIFFRACTIONr_chiral_restr0.0760.24179
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02128793
X-RAY DIFFRACTIONr_gen_planes_other0.020.024872
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_it0.6143.21213477
X-RAY DIFFRACTIONr_mcbond_other0.6143.21213476
X-RAY DIFFRACTIONr_mcangle_it1.1014.81616834
X-RAY DIFFRACTIONr_mcangle_other1.1014.81616835
X-RAY DIFFRACTIONr_scbond_it0.6153.36212617
X-RAY DIFFRACTIONr_scbond_other0.6153.36212614
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0375.00818531
X-RAY DIFFRACTIONr_long_range_B_refined2.57139.20428193
X-RAY DIFFRACTIONr_long_range_B_other2.55739.19628184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 274 -
Rwork0.312 5587 -
obs--98.37 %
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)
13.4043-2.3342-2.7091.77351.33815.32510.1065-0.0181-0.1044-0.1861-0.06930.1608-0.73010.0413-0.03720.58560.0687-0.07210.22540.01420.438833.986858.04114.2903
28.216-0.6197-0.25942.9808-0.84743.16060.06560.82410.3319-0.2747-0.0528-0.1408-0.2952-0.2845-0.01280.26660.07940.10820.12030.08210.172443.805863.5328-6.943
31.97160.4841-0.16722.25070.34082.55010.01730.20910.0578-0.3941-0.0318-0.5149-0.34480.10950.01450.1322-0.00770.12890.08890.05430.229658.094352.8494-2.2013
41.53380.0943-0.42482.07820.70632.2304-0.04680.13450.0216-0.2043-0.04260.0453-0.0678-0.05930.08940.06630.0382-0.0240.04970.0090.10934.155648.66599.0712
52.18610.0966-1.72251.39460.11682.64260.0158-0.12850.25890.0769-0.028-0.1341-0.35450.08540.01220.1062-0.0008-0.04720.03850.00650.322355.787469.313138.9843
61.8106-0.16840.13442.5735-0.46212.00450.044-0.13760.07270.22580.0480.1562-0.0641-0.0671-0.09190.02590.00540.00050.02-0.03230.146341.691958.786345.4991
71.42990.4611-1.21131.8652-0.26832.63690.0847-0.035-0.0017-0.0379-0.0333-0.31580.00470.2609-0.05140.06620.0418-0.03310.0843-0.00910.322766.160953.419437.9863
81.45491.7518-0.07353.9586-2.30592.9436-0.18530.2845-0.0576-0.52560.14360.06030.16880.09770.04160.31770.06150.00350.2558-0.02670.463463.582554.203319.2125
98.04970.32560.95165.1271-0.93863.6008-0.1120.23770.6342-0.09610.0853-0.17-0.59120.01860.02670.1127-0.00810.02310.01410.01830.252264.864868.993224.6587
102.6456-0.03321.56751.05540.28811.1706-0.1197-0.02540.13340.26160.08190.15040.27710.04920.03780.51130.016-0.00830.29340.07930.332447.678216.546249.2756
115.6275-1.8906-1.73281.11271.03442.9768-0.2991-0.467-0.38790.2528-0.037-0.05770.20710.16090.33610.2418-0.0033-0.1060.15430.10230.293965.484312.196352.0315
122.96930.0446-0.48051.14830.12181.03730.1329-0.27650.23460.1153-0.0462-0.2738-0.02210.1081-0.08670.08070.0025-0.05180.0387-0.02660.133158.739728.685748.0187
131.8940.75740.29963.69590.33331.6706-0.04380.0743-0.0566-0.118-0.0189-0.1190.1737-0.00150.06270.0302-0.0029-0.00080.0349-0.00270.052539.807620.879937.4254
146.2961-0.28033.41971.87280.02052.06270.047-0.01930.1615-0.0344-0.0275-0.26230.24890.0559-0.01950.31260.0721-0.00190.0622-0.05170.217457.45049.71998.1637
154.21391.0524-1.6745.7355-1.83352.8162-0.1281-0.0188-0.35720.1215-0.0413-0.25670.0443-0.11890.16950.09150.0294-0.04880.0375-0.05160.153542.97212.75447.7236
161.52430.17461.76142.05440.98232.34630.21190.0225-0.0937-0.002-0.06380.01940.22840.0113-0.14810.0544-0.03220.01860.10080.0340.238335.461310.530812.7724
171.65460.5317-1.22453.1051-0.35094.66890.04160.21760.0769-0.3637-0.03370.3213-0.0534-0.5059-0.00790.05020.018-0.03920.0774-0.01590.162733.11619.96362.2672
181.98550.19421.02672.1840.15392.54630.00490.24190.02050.00350.0037-0.3480.02240.3293-0.00860.03240.01340.04680.0672-0.00490.175963.60620.086411.3295
191.61630.69880.57321.14990.04731.79650.0539-0.1957-0.20240.2708-0.0361-0.02280.2506-0.1598-0.01780.1982-0.08910.05210.13220.01550.136946.872814.3523129.8597
2022.585514.132610.628215.660417.132821.1221-0.1055-0.2491-0.3962-0.4752-0.0431-0.0241-0.67350.01310.14860.2989-0.10460.08050.67790.09160.323842.25910.0483141.9992
212.4272-0.4239-0.1562.31580.25431.44060.0848-0.36020.12860.23650.0502-0.10370.20760.0346-0.1350.0846-0.03550.00130.14750.01290.069863.143725.7352131.8381
221.37070.36010.51591.74250.73912.56480.0428-0.15590.1683-0.0539-0.08370.1696-0.1082-0.07070.04090.0396-0.03890.02590.0746-0.00010.203137.714527.3031117.1787
238.1168-1.47011.36383.3997-0.08391.6759-0.0977-0.2726-0.56660.16260.10520.35910.2770.1054-0.00740.1508-0.02990.0350.07480.02930.116936.625310.9081116.8938
242.5350.17753.42121.30770.47765.022-0.08380.1145-0.0525-0.08110.0562-0.22920.18890.14420.02750.2785-0.00180.10250.23030.04040.249167.2749.342292.5038
256.84091.4842-0.46122.7799-0.32850.92080.11540.026-0.5751-0.17590.0999-0.25620.28370.078-0.21530.15960.0253-0.04410.0368-0.02250.166755.83551.46184.5282
262.60890.31750.83490.96410.25732.116-0.06330.34250.0538-0.22480.16060.0932-0.06660.182-0.09730.1119-0.051-0.00230.0660.00330.078855.160617.59384.3158
271.2426-0.30720.76044.324-0.63722.8433-0.1399-0.0172-0.06230.06410.1649-0.0891-0.14170.1601-0.0250.0179-0.0056-0.00010.0985-0.01760.098969.629619.5343103.4287
284.7375-1.1143-1.59171.50011.10743.0695-0.70240.11440.1594-0.68970.5520.5032-0.49590.23510.15050.766-0.386-0.33770.27040.26430.366751.560858.027877.0709
293.10820.5502-0.20993.1635-0.46192.76-0.60970.4378-0.0548-0.71560.4834-0.1767-0.07430.13120.12640.3865-0.26230.03070.1813-0.01860.089570.159551.430378.9881
307.21481.0304-1.91054.41031.51074.4816-0.57480.80260.2236-0.72660.35980.5357-0.0974-0.15380.2150.4044-0.2012-0.28120.16130.14650.227339.561145.916277.128
312.14730.1763-0.56214.22830.68261.4542-0.4013-0.04910.2991-0.3170.11080.6584-0.1712-0.07270.29050.228-0.0584-0.22940.08460.05850.294642.120452.551391.9676
326.05490.7304-0.71261.3801-0.29440.1690.0492-0.04470.1544-0.0098-0.03140.2167-0.104-0.0221-0.01780.20960.0302-0.02070.1468-0.06960.313555.921668.5781119.8586
330.9765-0.19180.05481.66090.14742.3223-0.0426-0.12950.14360.0042-0.09680.4488-0.1489-0.15160.13940.01550.0278-0.0380.095-0.07640.48939.577659.9824120.4488
345.34670.3506-1.44880.98980.80011.57150.2554-0.18950.53210.1402-0.15890.1701-0.0630.0226-0.09650.1488-0.00630.01470.1546-0.01150.222254.306858.3513128.9525
351.82560.3287-0.13952.308-0.13352.0152-0.0494-0.10280.0965-0.05230.01440.11120.0130.07290.03510.00360.00320.00910.0616-0.01620.14869.229151.1877115.2129
366.181.8506-1.42724.43530.5532.9984-0.06890.0010.7086-0.3268-0.02840.2158-0.18080.09330.09730.035-0.0076-0.01610.0268-0.00180.117969.465467.9088110.9213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 35
2X-RAY DIFFRACTION2A36 - 70
3X-RAY DIFFRACTION3A71 - 179
4X-RAY DIFFRACTION4A180 - 421
5X-RAY DIFFRACTION5B1 - 66
6X-RAY DIFFRACTION6B67 - 208
7X-RAY DIFFRACTION7B209 - 333
8X-RAY DIFFRACTION8B334 - 386
9X-RAY DIFFRACTION9B387 - 421
10X-RAY DIFFRACTION10C1 - 35
11X-RAY DIFFRACTION11C36 - 88
12X-RAY DIFFRACTION12C89 - 298
13X-RAY DIFFRACTION13C299 - 421
14X-RAY DIFFRACTION14D1 - 35
15X-RAY DIFFRACTION15D36 - 63
16X-RAY DIFFRACTION16D64 - 142
17X-RAY DIFFRACTION17D143 - 224
18X-RAY DIFFRACTION18D225 - 421
19X-RAY DIFFRACTION19E1 - 66
20X-RAY DIFFRACTION20E67 - 71
21X-RAY DIFFRACTION21E72 - 221
22X-RAY DIFFRACTION22E222 - 386
23X-RAY DIFFRACTION23E387 - 421
24X-RAY DIFFRACTION24F1 - 35
25X-RAY DIFFRACTION25F36 - 73
26X-RAY DIFFRACTION26F74 - 292
27X-RAY DIFFRACTION27F293 - 421
28X-RAY DIFFRACTION28G1 - 45
29X-RAY DIFFRACTION29G46 - 230
30X-RAY DIFFRACTION30G231 - 290
31X-RAY DIFFRACTION31G291 - 421
32X-RAY DIFFRACTION32H0 - 63
33X-RAY DIFFRACTION33H64 - 206
34X-RAY DIFFRACTION34H207 - 251
35X-RAY DIFFRACTION35H252 - 386
36X-RAY DIFFRACTION36H387 - 421

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