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- PDB-2v4a: Crystal structure of the SeMet-labeled prolyl-4 hydroxylase (P4H)... -

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Basic information

Entry
Database: PDB / ID: 2v4a
TitleCrystal structure of the SeMet-labeled prolyl-4 hydroxylase (P4H) type I from green algae Chlamydomonas reinhardtii.
ComponentsPROLYL-4 HYDROXYLASE
KeywordsHYDROLASE
Function / homologyq2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å
AuthorsKoski, M.K. / Hieta, R. / Bollner, C. / Kivirikko, K.I. / Myllyharju, J. / Wierenga, R.K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Active Site of an Algal Prolyl 4-Hydroxylase Has a Large Structural Plasticity.
Authors: Koski, M.K. / Hieta, R. / Bollner, C. / Kivirikko, K.I. / Myllyharju, J. / Wierenga, R.K.
History
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLYL-4 HYDROXYLASE
B: PROLYL-4 HYDROXYLASE
C: PROLYL-4 HYDROXYLASE
D: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,67415
Polymers105,9114
Non-polymers76311
Water5,639313
1
A: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7014
Polymers26,4781
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7625
Polymers26,4781
Non-polymers2844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6053
Polymers26,4781
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6053
Polymers26,4781
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.490, 137.490, 88.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PROLYL-4 HYDROXYLASE


Mass: 26477.760 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-TERMINALLY TRUNCATED CONSTRUCT STARTING FROM VAL-29 AND CONTAINING N-TERMINAL HIS-TAG
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Strain: CC125MT137C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI(DE3)

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Non-polymers , 5 types, 324 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsN-TERMINALLY TRUNCATED CONSTRUCT, STARTING FROM VAL29, TOGETHER WITH N-TERMINAL HIS-TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.5 %
Description: THE PHASES WERE SOLVED BY USING A MAD DATA COLLECTED TO 2.8A. THE HIGH RESOLUTION DATA SET TO 1.93A WAS COLLECTED FROM HIGH ENERGY REMOTE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9421, 0.9421, 0.9798
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94211
20.97981
ReflectionResolution: 1.93→25 Å / Num. obs: 457239 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 1.93→2.05 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0028refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.93→19.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.216 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3176 5 %RANDOM
Rwork0.188 ---
obs0.192 60331 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.93→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5773 0 41 313 6127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9548027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91224.291247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.122151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5481524
X-RAY DIFFRACTIONr_chiral_restr0.1050.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.22385
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.23884
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2372
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8751.53772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2425851
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.21132565
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0134.52176
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: 1.93→1.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 225
Rwork0.227 4277
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)
13.0590.1797-0.93452.3363-0.2241.79560.16070.43640.3063-0.2141-0.24670.1062-0.1308-0.26980.0861-0.02960.01070.0085-0.0282-0.0381-0.143484.429-45.6843.087
23.2432-1.4217-1.90472.24511.3794.11850.0136-0.13220.10490.21190.0064-0.0453-0.0153-0.1296-0.0201-0.124-0.0211-0.0175-0.0802-0.0404-0.129277.913-37.59118.281
33.9136-1.1094-0.20297.0817-3.34751.7238-0.0303-0.06430.05790.1639-0.0430.508-0.2083-0.72070.0732-0.0565-0.02310.03410.007-0.0613-0.083468.199-42.05415.199
45.9824-2.237-2.43511.30652.75125.62490.02840.23810.0783-0.2987-0.06650.3032-0.0707-0.18440.038-0.1594-0.0284-0.0326-0.0341-0.0081-0.158274.586-45.5515.202
52.5589-0.33550.75956.37245.816.6614-0.1173-0.0887-0.18340.1005-0.00460.05630.0855-0.07970.1218-0.0568-0.03150.0177-0.0750.0138-0.100978.179-49.89316.788
64.4571-3.9555-0.85096.21660.58990.94330.0024-0.28410.30010.12230.1431-0.41720.02410.1713-0.1454-0.1054-0.0388-0.01130.0012-0.0076-0.100291.763-41.92118.201
76.2324-3.81170.98045.36790.18952.2812-0.0117-0.43920.55940.16060.1184-0.9965-0.00830.3106-0.1068-0.1001-0.04030.0067-0.0086-0.02210.048297.053-41.62516.467
82.71791.1556-0.858123.90230.64234.6356-0.04220.1083-0.1206-0.50640.0022-0.31940.3659-0.06290.0401-0.0955-0.00910.0502-0.03930.002-0.1387.209-58.0078.384
91.1417-1.7565-0.450712.2876.18514.5366-0.1626-0.37980.12610.7590.3634-0.24050.31150.2359-0.2008-0.0287-0.0472-0.00780.08070.0079-0.116691.596-46.45521.297
101.13762.26721.49313.03916.98784.73360.054-0.1246-0.17660.4169-0.18650.19130.364-0.21550.1324-0.0927-0.04950.0526-0.0623-0.0186-0.11278.118-49.28115.411
117.7253-0.42620.14195.5468-0.48753.4261-0.02030.3579-0.2916-0.1701-0.10170.1070.06680.32470.1219-0.031-0.0074-0.0340.0211-0.0163-0.226653.406-18.43-0.31
126.5791-2.4023.78632.3824-2.02675.6058-0.1003-0.0424-0.17830.09280.0003-0.01560.20140.40550.0999-0.12890.03950.0317-0.0249-0.0082-0.094362.579-27.20811.425
1313.99984.2388-5.15314.2907-1.26519.775-0.3623-0.36510.57730.20950.2179-0.3031-0.3023-0.04050.14430.03070.0033-0.08880.1452-0.10480.013566.289-16.97318.382
147.4499-3.53323.54628.2675-3.35766.0641-0.04490.21630.13590.064-0.2562-0.44610.04280.54090.3011-0.1336-0.01150.03130.0791-0.0013-0.084466.961-19.4182.898
152.12730.2033-0.20684.6939-5.06258.1707-0.1583-0.1223-0.00290.27390.0123-0.1707-0.31360.32090.146-0.0369-0.0031-0.00530.0294-0.0703-0.008360.244-14.35412.085
167.1845-3.0398-0.18914.79820.05181.13610.0346-0.1741-0.3540.18860.07180.60950.0238-0.0706-0.1064-0.08680.00030.0353-0.0249-0.0175-0.04544.05-22.29814.269
177.6427-1.8984-1.56992.93631.05451.5503-0.0475-0.1749-0.22970.16170.15360.27560.03950.0747-0.1062-0.11810.0062-0.0063-0.0624-0.0252-0.079747.706-23.11211.688
183.10531.4173-1.31838.3746-0.50125.16830.1803-0.07670.13820.3158-0.2690.276-0.52210.0240.0886-0.0418-0.0191-0.0066-0.0396-0.037-0.149.055-6.8446.142
196.4402-1.8626-0.2160.91451.34334.3723-0.3675-0.7204-0.19340.35190.30.2070.3084-0.12340.0676-0.03020.06770.02160.075-0.0087-0.086653.081-24.02720.418
208.0281-0.82461.939614.2861-8.281417.45380.3138-0.24350.32320.5397-0.2886-0.1377-1.06091.2289-0.0251-0.0301-0.08950.03070.0347-0.0786-0.036962.408-8.1876.123
212.94151.622-0.7175.351-1.43215.0215-0.3582-0.13590.08590.52440.4420.57-0.4127-0.4531-0.08380.0527-0.0274-0.03920.08540.015-0.127347.042-13.38-7.993
223.4275-1.45931.70672.5742-0.91212.2537-0.0715-0.1145-0.0209-0.03480.13780.2848-0.2404-0.4952-0.0662-0.0292-0.0093-0.00590.0485-0.0118-0.091637.165-10.07-20.576
235.8093.89491.511322.721514.715624.9234-0.17950.4281-0.3746-0.19570.4162-0.96790.28670.616-0.23680.02430.0226-0.02980.08820.0215-0.037244.798-8.021-32.393
243.01020.2551.42272.4946-1.08225.0655-0.1554-0.01430.18410.04510.14750.0116-0.3937-0.23410.0079-0.02620.01280.005-0.04380.0028-0.10245.544-4.781-18.224
259.8267-1.7879-1.07350.5141-0.83675.758-0.87490.9639-0.385-1.47041.3557-1.7779-2.26470.7928-0.48090.42480.01350.0120.15570.0510.443160.127-8.706-25.087
2615.05866.46114.716811.19252.46478.30970.10570.20740.1845-0.2795-0.1213-0.2597-0.36560.18420.0157-0.0297-0.01220.0046-0.07870.0003-0.111156.081-9.5-18.877
276.9071-1.28821.27895.83620.77374.93830.24120.0914-1.0625-0.28390.2109-0.00281.0631-0.0394-0.45210.2716-0.109-0.03580.0172-0.01650.031445.835-27.031-22.122
2816.70970.4362.3610.6366-0.2482.1791-0.22430.031-0.3401-0.12680.1709-0.00150.17670.04480.0534-0.0008-0.05560.0256-0.06430.0163-0.074353.12-18.137-16.126
298.6277-3.46232.33892.3733-1.5195.27030.27470.2669-0.6019-0.724-0.13330.6490.56620.0435-0.14140.4201-0.1236-0.07760.0642-0.0867-0.011742.567-23.322-29.174
307.42742.40414.46832.23570.72275.8918-0.11880.10690.0647-0.24810.1292-0.1303-0.45090.0599-0.0104-0.0187-0.04080.0083-0.0788-0.003-0.091250.186-8.481-20.983
3123.4210.49624.628110.5080.496313.2769-0.01850.4861-1.4776-0.09120.3706-0.98010.21252.2781-0.3520.45860.13840.03840.5451-0.09520.233820.619-0.6-2.815
324.4597-3.7239-1.1864.93411.61923.506-0.0343-0.0120.58140.14860.1036-0.52410.05580.6281-0.0692-0.06870.04560.01930.0890.03340.015722.64912.926-9.284
3310.9086-1.95860.50038.4598-1.53678.60850.60310.7905-0.1384-0.9822-0.622-0.34980.17760.45420.01890.36090.26880.04950.4144-0.0808-0.040921.1592.077-26.733
345.0019-1.3258-0.942.9168-0.21475.10860.26670.4467-0.3064-0.2339-0.189-0.01320.43310.445-0.07770.010.1671-0.03550.0528-0.0651-0.047117.8321.99-13.626
3520.80815.4656-7.767217.9928-8.491211.284-0.27330.7871-0.8182-0.6006-0.1219-0.70780.4694-0.08760.39530.25030.1598-0.03070.41160.03060.21722.50510.953-20.213
3615.4684-1.6872-7.3195.144-1.51747.64150.34210.3553-0.3143-0.3445-0.13120.1570.0824-0.0255-0.21090.03050.1166-0.0479-0.032-0.003-0.05459.0967.698-13.128
378.8202-4.92260.28768.2115-0.72482.01870.18940.4611.5624-0.2407-0.065-0.8827-0.66160.3748-0.12440.1909-0.00750.07780.21280.18490.263719.89324.5-18.85
389.5963-0.5915-2.59552.17420.40582.77170.08720.45620.45-0.14690.0382-0.2325-0.22140.0563-0.12530.00830.03890.00970.00840.0481-0.014612.30817.872-12.695
394.714-3.82640.1565.69-1.27886.65370.62490.90880.7569-0.8345-0.6318-0.7758-0.30940.77690.00690.14930.18730.14880.37560.13520.038321.73515.033-24.145
4019.58651.9055-7.222610.90150.51118.8249-0.04310.5072-0.5573-0.49530.0380.77790.1483-0.2060.00520.00020.083-0.0967-0.035-0.0446-0.00556.7593.233-11.729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 51
2X-RAY DIFFRACTION2A52 - 99
3X-RAY DIFFRACTION3A100 - 108
4X-RAY DIFFRACTION4A109 - 123
5X-RAY DIFFRACTION5A124 - 165
6X-RAY DIFFRACTION6A166 - 184
7X-RAY DIFFRACTION7A185 - 210
8X-RAY DIFFRACTION8A211 - 220
9X-RAY DIFFRACTION9A221 - 236
10X-RAY DIFFRACTION10A237 - 249
11X-RAY DIFFRACTION11B28 - 51
12X-RAY DIFFRACTION12B52 - 73
13X-RAY DIFFRACTION13B74 - 102
14X-RAY DIFFRACTION14B103 - 123
15X-RAY DIFFRACTION15B124 - 166
16X-RAY DIFFRACTION16B167 - 194
17X-RAY DIFFRACTION17B195 - 211
18X-RAY DIFFRACTION18B212 - 227
19X-RAY DIFFRACTION19B228 - 241
20X-RAY DIFFRACTION20B242 - 249
21X-RAY DIFFRACTION21C28 - 50
22X-RAY DIFFRACTION22C51 - 74
23X-RAY DIFFRACTION23C75 - 100
24X-RAY DIFFRACTION24C101 - 135
25X-RAY DIFFRACTION25C152 - 156
26X-RAY DIFFRACTION26C157 - 166
27X-RAY DIFFRACTION27C167 - 202
28X-RAY DIFFRACTION28C203 - 226
29X-RAY DIFFRACTION29C227 - 236
30X-RAY DIFFRACTION30C237 - 249
31X-RAY DIFFRACTION31D28 - 38
32X-RAY DIFFRACTION32D39 - 67
33X-RAY DIFFRACTION33D68 - 100
34X-RAY DIFFRACTION34D101 - 135
35X-RAY DIFFRACTION35D140 - 155
36X-RAY DIFFRACTION36D156 - 167
37X-RAY DIFFRACTION37D168 - 195
38X-RAY DIFFRACTION38D196 - 227
39X-RAY DIFFRACTION39D228 - 242
40X-RAY DIFFRACTION40D243 - 249

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