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- PDB-4a2c: Crystal structure of galactitol-1-phosphate dehydrogenase from Es... -

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Basic information

Entry
Database: PDB / ID: 4a2c
TitleCrystal structure of galactitol-1-phosphate dehydrogenase from Escherichia coli
ComponentsGALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / METAL BINDING-SITE
Function / homology
Function and homology information


galactitol-1-phosphate 5-dehydrogenase / galactitol-1-phosphate 5-dehydrogenase activity / galactitol catabolic process / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Galactitol 1-phosphate 5-dehydrogenase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsAlvarez, Y. / Esteban-Torres, M. / Acebron, I. / de las Rivas, B. / Munoz, R. / Mancheno, J.M.
CitationJournal: FEBS Lett. / Year: 2012
Title: The Crystal Structure of Galactitol-1-Phosphate 5-Dehydrogenase from Escherichia Coli K12 Provides Insights Into its Anomalous Behavior on Imac Processes
Authors: Esteban-Torres, M. / Alvarez, Y. / Acebron, I. / De Las Rivas, B. / Munoz, R. / Kohring, G.-W. / Roa, A.M. / Sobrino, M. / Mancheno, J.M.
History
DepositionSep 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE
B: GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1677
Polymers74,8602
Non-polymers3075
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-45.4 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.720, 77.140, 107.510
Angle α, β, γ (deg.)90.00, 95.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE / / GALACTITOL-1-PHOSPHATE DEHYDROGENASE


Mass: 37430.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A9S3, galactitol-1-phosphate 5-dehydrogenase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 6.5 / Details: PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.87→29.8 Å / Num. obs: 56481 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.2
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.5 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DQ4
Resolution: 1.87→28.952 Å / SU ML: 0.6 / σ(F): 1.38 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2729 2862 5.1 %
Rwork0.2127 --
obs0.2158 56448 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.946 Å2 / ksol: 0.343 e/Å3
Refinement stepCycle: LAST / Resolution: 1.87→28.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 5 608 5867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075427
X-RAY DIFFRACTIONf_angle_d1.1277374
X-RAY DIFFRACTIONf_dihedral_angle_d16.0771982
X-RAY DIFFRACTIONf_chiral_restr0.084846
X-RAY DIFFRACTIONf_plane_restr0.005958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90220.33681200.27312508X-RAY DIFFRACTION89
1.9022-1.93680.34591290.26022491X-RAY DIFFRACTION91
1.9368-1.97410.28291220.24062591X-RAY DIFFRACTION91
1.9741-2.01440.26961350.22062529X-RAY DIFFRACTION92
2.0144-2.05810.31011300.22492583X-RAY DIFFRACTION93
2.0581-2.1060.26981450.23082592X-RAY DIFFRACTION94
2.106-2.15870.30221340.21952662X-RAY DIFFRACTION95
2.1587-2.2170.26551440.20992611X-RAY DIFFRACTION95
2.217-2.28220.31641450.21972665X-RAY DIFFRACTION95
2.2822-2.35580.291570.21532645X-RAY DIFFRACTION96
2.3558-2.440.29391350.21462707X-RAY DIFFRACTION96
2.44-2.53760.30411420.21362708X-RAY DIFFRACTION97
2.5376-2.65310.2851530.20872686X-RAY DIFFRACTION98
2.6531-2.79280.29311530.20582750X-RAY DIFFRACTION99
2.7928-2.96760.29611480.20722795X-RAY DIFFRACTION99
2.9676-3.19650.22661320.20012794X-RAY DIFFRACTION100
3.1965-3.51770.27131560.20232801X-RAY DIFFRACTION100
3.5177-4.02550.28031750.19542807X-RAY DIFFRACTION100
4.0255-5.06730.22421620.18132788X-RAY DIFFRACTION100
5.0673-28.95570.24891450.2532873X-RAY DIFFRACTION100
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)
10.04790.1354-0.38732.39970.07733.7999-0.15640.51330.0083-0.60770.51370.63260.4292-1.2194-0.34420.6264-0.3096-0.10870.57490.1580.336117.1725-12.6583-14.1505
22.07872.2516-0.50425.7864-1.87452.4670.0270.27540.1921-0.47530.0993-0.0840.1014-0.0674-0.12620.2450.01310.07620.15660.05130.147430.2265-8.0435-5.1122
39.2155-0.10732.53540.43931.15073.87570.22080.21630.3765-0.41030.22460.9744-0.3641-0.6024-0.41290.30090.1010.00560.40130.16540.51597.9578-14.0138-1.8039
41.84871.5548-0.48352.2356-0.30482.74960.00390.31730.2909-0.26970.02140.007-0.1443-0.412-0.02290.28490.10.0950.20150.05530.229423.5301-9.7485-3.9424
52.8475-0.3547-1.684.58971.10244.0124-0.107-0.1144-0.1333-0.1446-0.1765-0.544-0.10220.66530.24370.19030.03470.04250.24080.08170.197633.7032-8.46782.9364
67.16681.4822-1.33767.06631.06443.69250.00940.2250.0859-0.5124-0.0507-0.1537-0.23440.03430.06150.23960.01160.06930.1270.03280.154221.44152.352813.3873
79.08271.16254.15185.0470.94716.57580.31010.13510.8991-0.2881-0.50970.3805-0.6564-0.70910.17650.38010.21360.19250.3550.05730.398218.4821-5.0622-0.9158
81.72980.0243-0.47593.1515-0.22951.7629-0.0645-0.1963-0.1938-0.4179-0.2447-0.44710.26910.24910.25330.15560.03090.08990.19160.08980.228429.7644-15.18161.2708
95.358-1.9241-2.69616.78333.77116.35180.12980.0433-0.1331-0.15330.03140.3414-0.3362-0.1531-0.14330.10030.0003-0.00410.12520.03110.140620.6049-15.787615.6567
100.38390.4581-0.86473.7001-0.96893.4224-0.00380.1117-0.31930.2862-0.1737-0.12290.24180.22020.16060.07330.04720.0360.1477-0.01660.1816.3988-21.398523.3834
110.96510.5759-0.39121.9598-0.00122.0411-0.18970.0257-0.33180.019-0.1348-0.07110.38260.10830.21960.1790.05090.07830.1076-0.02580.209415.538-27.284118.7043
121.7066-1.2567-1.26371.17721.59452.6838-0.1203-0.0752-0.11770.4435-0.17940.21110.4617-0.38490.24060.3366-0.07380.16330.1482-0.0750.28886.8454-32.324319.9295
135.79385.91725.74666.79555.05736.57320.0803-0.3379-0.51650.4851-0.1410.02990.6919-0.55720.02630.321-0.02810.14910.15710.00580.25457.9285-28.771234.2022
142.4917-0.6079-0.68632.0523-1.45362.7227-0.01480.0984-0.26290.0344-0.10070.3141-0.0546-0.32130.10510.13370.01270.02780.133-0.06820.17116.2668-18.871524.117
152.4111-0.09530.67430.5409-0.1032.08720.05570.36750.0213-0.1288-0.08950.19340.1151-0.3162-0.01280.09390.0208-0.13240.2506-0.1340.2845-1.4236-12.729121.9357
163.43751.2021-3.1313.2079-1.63557.17880.060.10530.0154-0.2207-0.0775-0.0356-0.1972-0.13270.00250.1186-0.0001-0.01110.0636-0.02230.097112.88-10.69322.6108
172.66991.72230.93685.88271.8213.164-0.1612-0.003-0.2416-0.17010.2452-0.49910.4560.2014-0.07380.18670.03270.04640.13570.05150.141227.2429-21.46111.4772
182.64281.6416-2.64242.6215-1.78082.655-0.34970.58980.1199-0.58560.24490.16270.4475-0.4494-0.00440.742-0.29830.08290.3716-0.00760.254415.9025-24.1477-10.0652
191.44211.0080.03248.8288-5.98584.4446-0.8223-1.20550.3390.99071.09910.5908-0.9563-1.1529-0.2160.34470.1846-0.00770.6347-0.25850.68316.0637-23.4222-1.5055
205.5859-0.0859-2.98072.7512-0.02872.0123-0.05280.32230.2334-0.45240.1297-0.13610.1173-0.1495-0.06290.5125-0.1008-0.03340.11580.06880.173321.341-23.4336-3.88
211.044-0.72420.88422.89510.32441.1819-0.14740.02490.1513-0.2280.04560.7322-0.0105-0.48760.07640.1238-0.1005-0.01670.42030.14030.325-16.5245-8.303459.4006
222.8124-1.42041.74885.8584-2.55196.0880.12720.136-0.09830.0382-0.11570.06420.25550.1182-0.0190.0496-0.04820.00050.20940.00050.1098-4.0388-7.307258.8674
230.24490.1320.25911.3386-0.36640.6046-0.02270.2465-0.0418-0.28660.00650.28970.0463-0.2322-0.08810.2425-0.0864-0.36220.34930.03080.4138-15.9697-8.980746.064
241.40090.7562-0.39482.46060.63213.06770.0477-0.2921-0.18710.496-0.1745-0.18570.02820.4110.10550.2052-0.0735-0.05170.22550.03660.16042.1413-7.464962.3368
256.615-2.54444.11848.63780.71523.25570.01130.075-0.14370.30280.16050.20920.1499-0.0212-0.17530.19680.00150.06370.1680.05030.1687.0447-20.478646.0849
269.5455-1.57570.33387.7428-3.76631.85240.04780.6095-0.5097-0.6732-0.39670.55520.5545-0.66580.32970.2281-0.0532-0.06150.2403-0.05810.1923-6.0444-13.75250.8031
272.59380.43550.16283.4328-0.35221.72620.0717-0.11470.1840.5462-0.1273-0.206-0.1480.18770.0380.1696-0.0536-0.05160.18610.01970.10760.6154-2.540859.2416
280.10730.1395-0.59912.8617-0.7533.4153-0.014-0.0106-0.00890.018-0.1921-0.0518-0.10960.05430.21280.0851-0.002-0.03140.1002-0.01460.09788.00952.899239.6762
293.9551-2.28370.17943.81510.38442.14760.1850.08520.16050.0188-0.2115-0.0552-0.1724-0.27220.03650.16510.0564-0.0160.1079-0.02520.11242.120313.306735.1325
300.1710.11840.1060.49980.94191.87190.06590.1365-0.0207-0.2148-0.08450.0802-0.1165-0.07470.09970.36080.3017-0.22220.2611-0.06260.19260.734712.885124.5865
318.2234-4.67973.90315.6943-1.85145.2280.05740.55160.6027-0.432-0.1081-0.2939-0.14630.30060.11370.31710.070.00890.15840.08730.185511.565910.901220.8408
322.66990.4451-0.40311.9805-0.07491.4038-0.02720.06950.1447-0.3821-0.25040.2428-0.1481-0.30670.19770.12690.0569-0.0460.1575-0.06470.12864.0349-0.017327.4268
332.74350.91620.13320.7398-0.06440.03430.07360.03730.3837-0.1255-0.16370.3337-0.1956-0.42860.08410.19490.0917-0.10390.3131-0.10270.2605-1.706-6.663620.1679
345.65390.2634-4.12933.0925-1.41714.7627-0.07050.0291-0.0952-0.3546-0.3086-0.00510.2141-0.01530.35230.10060.0591-0.03560.1191-0.05210.17078.2581-6.402226.6082
353.3725-4.67263.64896.4726-5.0553.9475-0.0791-0.0463-0.39130.0219-0.032-0.27640.41010.18280.10290.1626-0.0075-0.00930.23290.04120.22447.8385-10.382547.8753
363.79783.46640.71574.51262.46832.5775-0.036-0.1803-0.15130.27160.1451-0.68030.02110.6314-0.11280.1033-0.0234-0.05320.24430.02660.16711.2623-1.546350.4263
370.69130.35-0.94422.2193-0.93841.92260.0821-0.28210.46830.32080.0753-0.0405-0.12560.1228-0.12350.2077-0.0587-0.02860.1595-0.06130.14440.363410.633352.0309
381.38320.7040.3431.61920.57230.2103-0.0897-0.2169-0.02280.0727-0.14550.6532-0.0677-0.47770.19940.0965-0.0041-0.00330.45040.0290.3809-18.47953.996854.2008
392.57040.54961.2190.38720.91422.1617-0.48860.70481.3448-0.23180.26130.2538-0.44830.03770.27830.2783-0.0442-0.25180.27410.01730.5288-17.12417.329943.2545
405.4514-0.4524-0.4573.81714.21894.66360.1885-0.260.10480.4365-0.28430.17540.0697-0.13380.09470.223-0.0047-0.00780.10730.01560.1849-8.98665.118755.2039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:20)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 21:37)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 38:49)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 50:71)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 72:88)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 89:106)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 107:114)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 115:143)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 144:154)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 155:171)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 172:195)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 196:221)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 222:229)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 230:258)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 259:277)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 278:292)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 293:319)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 320:332)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 333:340)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 341:346)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 1:24)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 25:41)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 42:57)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 58:87)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 88:105)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 106:114)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 115:143)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 144:183)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 184:205)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 206:220)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 221:228)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 229:262)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 263:277)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 278:287)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 288:294)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 295:305)
37X-RAY DIFFRACTION37(CHAIN B AND RESID 306:322)
38X-RAY DIFFRACTION38(CHAIN B AND RESID 323:331)
39X-RAY DIFFRACTION39(CHAIN B AND RESID 332:340)
40X-RAY DIFFRACTION40(CHAIN B AND RESID 341:346)

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