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- PDB-3n2l: 2.1 Angstrom resolution crystal structure of an Orotate Phosphori... -

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Basic information

Entry
Database: PDB / ID: 3n2l
Title2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / Orotate Phosphoribosyltransferase / Pyrimidine Ribonucleotide Biosynthesis / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Glycosyltransferase / Magnesium / Pyrimidine biosynthesis
Function / homology
Function and homology information


pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleotide biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHalavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / 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 / _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: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
C: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase
E: Orotate phosphoribosyltransferase
F: Orotate phosphoribosyltransferase
G: Orotate phosphoribosyltransferase
H: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,54411
Polymers210,4388
Non-polymers1063
Water11,512639
1
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6453
Polymers52,6092
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-25 kcal/mol
Surface area18280 Å2
MethodPISA
2
C: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)52,6092
Polymers52,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-13 kcal/mol
Surface area17530 Å2
MethodPISA
3
E: Orotate phosphoribosyltransferase
F: Orotate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)52,6092
Polymers52,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-12 kcal/mol
Surface area18140 Å2
MethodPISA
4
G: Orotate phosphoribosyltransferase
H: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6804
Polymers52,6092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-36 kcal/mol
Surface area17340 Å2
MethodPISA
5
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
C: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2545
Polymers105,2194
Non-polymers351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-49 kcal/mol
Surface area31670 Å2
MethodPISA
6
E: Orotate phosphoribosyltransferase
F: Orotate phosphoribosyltransferase
G: Orotate phosphoribosyltransferase
H: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2906
Polymers105,2194
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-58 kcal/mol
Surface area31220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.587, 76.712, 133.944
Angle α, β, γ (deg.)90.00, 92.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Orotate phosphoribosyltransferase / OPRT / OPRTase


Mass: 26304.713 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: El Tor Inaba N16961 / Gene: pyrE, VC_0211 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPLus
References: UniProt: Q9KVD5, orotate phosphoribosyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 7.5 mg/mL protein in 10 mM Tris/HCl pH 8.3 0.5 M NaCl, 5 mM BME. The crystallization condition is The Classics II Suite (#8) Cryo 5M NaCl + 50% sucrose. Crystals grew from 1:1 v/v drop. , ...Details: 7.5 mg/mL protein in 10 mM Tris/HCl pH 8.3 0.5 M NaCl, 5 mM BME. The crystallization condition is The Classics II Suite (#8) Cryo 5M NaCl + 50% sucrose. Crystals grew from 1:1 v/v drop. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2010 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 114128 / Num. obs: 114128 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.25
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.72 / Num. unique all: 5630 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LH0
Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.609 / SU ML: 0.102 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26861 5711 5 %RANDOM
Rwork0.222 ---
obs0.22436 108289 99.51 %-
all-108289 --
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: 44.833 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0 Å20.7 Å2
2---2.37 Å20 Å2
3---3.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11639 0 3 639 12281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211976
X-RAY DIFFRACTIONr_bond_other_d0.0010.028111
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.96416158
X-RAY DIFFRACTIONr_angle_other_deg0.867319693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.74851487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.68123.902569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.357152077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4861586
X-RAY DIFFRACTIONr_chiral_restr0.1010.21841
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022556
X-RAY DIFFRACTIONr_mcbond_it0.8371.57426
X-RAY DIFFRACTIONr_mcbond_other0.2091.53075
X-RAY DIFFRACTIONr_mcangle_it1.504211884
X-RAY DIFFRACTIONr_scbond_it2.26534550
X-RAY DIFFRACTIONr_scangle_it3.5764.54274
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 384 -
Rwork0.292 7873 -
obs-7873 98.15 %
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)
15.13940.12190.1693.81470.49493.4574-0.0311-0.73250.15390.7450.1013-0.1833-0.07260.0483-0.07020.35280.049-0.04270.391-0.02960.047940.4369-10.094350.1849
21.9732-0.095-0.241.3394-0.61361.9817-0.0048-0.32210.16920.35790.04130.143-0.1336-0.0841-0.03660.21720.03220.00110.2282-0.03610.112635.7483-8.145338.6425
33.0791-0.2981-0.17113.5266-0.40853.18490.03540.0290.44830.01590.05740.0846-0.2378-0.5012-0.09280.12890.05780.00280.27510.01010.236127.0291-3.916129.2197
44.8426-1.55980.80761.3915-0.32040.7809-0.001-0.52280.12550.35510.0680.3965-0.006-0.1762-0.0670.37740.04020.06770.4488-0.03290.280323.0408-6.552244.5638
526.1273-5.90645.96247.4694-1.9128.1868-0.0341-1.54540.65050.79530.0715-0.13760.1009-0.2604-0.03750.56680.1296-0.09810.6125-0.03550.096956.9866-23.9563.4303
65.6016-0.85611.19233.9965-0.86835.6620.02710.35770.1664-0.53350.0173-0.1556-0.2248-0.112-0.04440.2906-0.0230.06440.2420.04160.096142.9562-2.18828.3991
72.2440.58420.07232.6344-0.09692.6524-0.0219-0.0070.29850.06610.0229-0.2791-0.2494-0.008-0.0010.12590.0153-0.01060.0901-0.00310.180845.6167-0.468926.6959
82.6865-3.6054-0.24398.54111.7567.17530.07670.19770.1374-0.1949-0.0921-0.0326-0.9484-0.02520.01540.3327-0.02490.01510.09750.01410.324147.870913.555826.3372
91.31251.6451.32465.83595.41945.0991-0.1550.43540.7506-1.30230.25780.0527-1.34750.1714-0.10280.7766-0.07330.0650.44770.19970.743650.703211.951913.948
101.9649-0.62120.17410.89571.91896.1647-0.04810.31770.2149-0.25410.1774-0.2113-0.34890.7412-0.12930.5341-0.07270.13570.39120.03910.371650.4865-1.70887.7114
114.1708-0.33050.15832.7774-2.1795.62-0.0939-0.91030.0340.75190.2659-0.07840.28620.2568-0.1720.44360.1226-0.12780.48120.01580.088553.7421-26.362952.8629
122.6340.0355-0.53241.46480.39162.5455-0.0093-0.1498-0.10840.20640.0136-0.5288-0.01570.2276-0.00430.12140.0346-0.05310.17980.02320.274358.2838-27.19934.35
134.6737-0.96580.8433.66980.41632.4638-0.0420.1063-0.38270.08480.1365-0.48590.30820.593-0.09450.18650.1041-0.03240.32090.00440.511471.4086-33.734832.6347
143.7402-1.7146-1.04151.4816-0.13370.8593-0.2193-0.83270.45340.25170.1749-0.5074-0.07220.34320.04440.37030.0756-0.15520.6263-0.04970.449567.0519-26.121850.0706
1526.8886-9.53023.571613.6786-0.36814.5233-0.3039-1.1113-0.37660.61250.21260.00070.0127-0.060.09130.6390.08490.02310.6613-0.06070.026234.4119-10.127162.7782
160.7305-0.3020.44733.82032.03315.02930.13970.370.0102-0.33040.0764-0.2720.09110.2324-0.2160.29280.03820.07140.286-0.02030.200852.9442-33.368912.6676
172.9605-0.39530.49914.4793-0.24042.619-0.0611-0.0512-0.40730.12840.007-0.2620.1643-0.09260.05410.135-0.0020.03090.0940.02760.188846.4566-35.90930.0682
183.03270.3275-0.65875.3616-1.07074.66930.07710.1179-0.56980.0655-0.0023-0.15320.614-0.1904-0.07480.2692-0.0297-0.01290.07960.00120.347345.0396-46.923227.6786
191.27044.0564-3.374114.3928-12.100910.18560.04290.4231-0.035-0.5330.60420.75740.4638-0.3709-0.64710.96280.0325-0.13740.8124-0.31220.910841.4916-50.829516.9911
203.47941.0233-2.15674.3372-2.65765.9522-0.01360.5554-0.4319-0.52020.2234-0.01550.192-0.6778-0.20990.35310.02580.04340.3199-0.07090.147943.4851-36.74959.1641
213.58460.2353-0.30062.5299-0.36935.15010.02990.76160.3042-0.57820.05750.0987-0.40830.0602-0.08730.313-0.0542-0.03250.35370.08150.12526.5602-46.024914.9712
222.64530.3020.25892.49980.44491.979-0.00070.02770.2197-0.10930.0508-0.1531-0.06920.2684-0.05010.1074-0.03080.00980.1490.00820.143512.1186-46.366835.2027
238.57152.73143.44496.92741.27662.779-0.1184-0.12921.1086-0.09460.0207-0.3473-0.53350.2280.09760.2499-0.07060.09970.4086-0.03030.392624.3483-39.24832.1599
245.0232.18061.81141.56250.02041.7833-0.28060.7344-0.1098-0.31660.2589-0.1835-0.05630.26910.02170.3916-0.05090.07040.4642-0.00020.314120.174-46.780317.8142
2524.06524.97832.81245.84132.84626.224-0.22021.02050.2561-0.90990.19570.2721-0.15630.08230.02450.5477-0.0787-0.1490.60690.05140.1093-11.8014-62.32473.6038
263.8247-0.81431.17714.31811.36254.9019-0.0542-0.25580.26940.32720.1126-0.0066-0.25030.1757-0.05840.30170.01010.08350.2124-0.04050.12592.7924-39.937158.3803
271.4571-0.5892-0.06592.9768-0.02712.19-0.003-0.01410.328-0.1202-0.00090.252-0.1919-0.01980.00380.1292-0.011-0.01470.0946-00.2029-0.4139-38.730740.1931
282.40560.33511.22866.8841-1.64056.0069-0.0365-0.22350.45840.2417-0.07370.2227-0.9380.03120.11030.35390.01360.00750.0928-0.01020.3463-2.5465-25.151240.8864
2911.0363-6.57035.99915.0702-5.20875.577-0.611-0.86990.74111.44230.607-0.1485-1.8577-0.63540.0041.16050.15410.04220.4414-0.17320.7937-5.6695-27.542654.9187
302.8332-0.09881.20361.9155-1.07924.9037-0.0954-0.34930.35880.55850.1710.4705-0.2744-0.369-0.07560.33370.04110.13730.2575-0.04530.2389-5.4344-37.665157.5585
312.17850.2401-0.85882.61630.70665.9525-0.12470.7531-0.0785-0.63970.17140.2570.2694-0.2587-0.04670.3153-0.1037-0.14010.4363-0.03250.1788-8.4173-64.637314.0958
323.2855-0.10640.10882.5705-0.37422.2786-0.00290.114-0.1297-0.10050.0440.61170.0768-0.2819-0.04110.1005-0.0389-0.0360.1368-0.01890.2768-14.334-66.582833.6421
335.00011.0119-1.53611.7841-0.94862.2714-0.13960.4153-0.3227-0.28620.16050.18950.2541-0.4642-0.02090.1467-0.0865-0.1180.3627-0.03920.4051-25.4902-70.001126.2962
342.60860.8176-1.38491.46790.1050.9841-0.16510.69930.4373-0.39980.15030.7638-0.0912-0.35270.01480.3241-0.1008-0.18460.6160.09760.4466-19.8726-61.980916.3541
3528.331910.47433.0586.24951.6479.8685-0.52161.41380.6543-0.94490.5470.31350.27890.105-0.02540.5491-0.0571-0.04690.53920.06070.020212.1279-47.99163.869
362.96810.0085-0.0382.9592-1.10825.9830.1547-0.31370.09760.3060.01410.35440.1079-0.1925-0.16880.2819-0.03530.0890.21920.00920.1083-7.0259-72.714556.1579
372.677-0.3023-0.29823.11690.36662.6940.0080.0257-0.3302-0.0405-0.02720.17540.204-0.00610.01910.1364-0.00650.01950.06870.00180.208-2.6696-72.938237.9457
382.65690.325-0.26766.24160.29324.12640.1131-0.0219-0.4211-0.04670.01390.05470.62180.1697-0.1270.24530.0441-0.00880.09460.00160.32910.1536-85.304239.3373
391.6438-1.8141.575512.32087.08859.15210.0293-0.3346-0.28450.69320.4595-0.10310.4958-0.0809-0.48880.7629-0.0068-0.03380.65270.11540.60813.6139-89.278150.1651
401.9822-0.8539-2.09473.03443.43957.8029-0.0644-0.624-0.40190.73240.3732-0.2560.40150.8732-0.30870.4290.01050.02630.38140.02990.25531.837-75.211257.6892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 27
2X-RAY DIFFRACTION2A28 - 90
3X-RAY DIFFRACTION3A91 - 134
4X-RAY DIFFRACTION4A135 - 193
5X-RAY DIFFRACTION5A194 - 214
6X-RAY DIFFRACTION6B1 - 36
7X-RAY DIFFRACTION7B37 - 129
8X-RAY DIFFRACTION8B130 - 152
9X-RAY DIFFRACTION9B153 - 175
10X-RAY DIFFRACTION10B176 - 194
11X-RAY DIFFRACTION11C2 - 36
12X-RAY DIFFRACTION12C37 - 100
13X-RAY DIFFRACTION13C101 - 149
14X-RAY DIFFRACTION14C150 - 194
15X-RAY DIFFRACTION15C195 - 214
16X-RAY DIFFRACTION16D2 - 50
17X-RAY DIFFRACTION17D51 - 116
18X-RAY DIFFRACTION18D117 - 156
19X-RAY DIFFRACTION19D157 - 175
20X-RAY DIFFRACTION20D176 - 194
21X-RAY DIFFRACTION21E2 - 36
22X-RAY DIFFRACTION22E37 - 123
23X-RAY DIFFRACTION23E124 - 148
24X-RAY DIFFRACTION24E149 - 193
25X-RAY DIFFRACTION25E194 - 214
26X-RAY DIFFRACTION26F2 - 36
27X-RAY DIFFRACTION27F37 - 129
28X-RAY DIFFRACTION28F130 - 153
29X-RAY DIFFRACTION29F154 - 173
30X-RAY DIFFRACTION30F174 - 194
31X-RAY DIFFRACTION31G2 - 36
32X-RAY DIFFRACTION32G37 - 118
33X-RAY DIFFRACTION33G119 - 169
34X-RAY DIFFRACTION34G170 - 196
35X-RAY DIFFRACTION35G197 - 214
36X-RAY DIFFRACTION36H2 - 41
37X-RAY DIFFRACTION37H42 - 116
38X-RAY DIFFRACTION38H117 - 156
39X-RAY DIFFRACTION39H157 - 175
40X-RAY DIFFRACTION40H176 - 194

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