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- PDB-6bal: 2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 6bal
Title2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae in Complex with L-Malate
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Malate Dehydrogenase / L-Malate
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain ...Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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
(2S)-2-hydroxybutanedioic acid / Malate dehydrogenase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Satchell, K.J.F. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae in Complex with L-Malate
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Satchell, K.J.F. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
E: Malate dehydrogenase
F: Malate dehydrogenase
G: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,28426
Polymers282,5488
Non-polymers73718
Water23,0591280
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9137
Polymers70,6372
Non-polymers2765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-24 kcal/mol
Surface area23530 Å2
MethodPISA
2
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8147
Polymers70,6372
Non-polymers1775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-25 kcal/mol
Surface area23680 Å2
MethodPISA
3
E: Malate dehydrogenase
F: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8147
Polymers70,6372
Non-polymers1775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-24 kcal/mol
Surface area24060 Å2
MethodPISA
4
G: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7435
Polymers70,6372
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-24 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.108, 78.079, 114.029
Angle α, β, γ (deg.)71.09, 75.44, 68.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Malate dehydrogenase


Mass: 35318.438 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: mdh, HI_1210 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P44427, malate dehydrogenase
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1280 / 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: 1.9 Å3/Da / Density % sol: 35.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 20.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5; Screen: 0.2M Ammonium formate, 20% (w/v) PEG3350, 0.25mM DL-Malic acid; Cryo: paratone.

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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: Apr 20, 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: 2.1→30 Å / Num. obs: 126522 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.054 / Rrim(I) all: 0.108 / Rsym value: 0.093 / Χ2: 1.021 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6257 / CC1/2: 0.665 / Rpim(I) all: 0.392 / Rrim(I) all: 0.77 / Rsym value: 0.662 / Χ2: 1.019 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HHP
Resolution: 2.1→29.75 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.591 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21869 6277 5 %RANDOM
Rwork0.16958 ---
obs0.17202 120245 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.765 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.88 Å2-0.44 Å2
2--0.27 Å20.77 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 2.1→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18305 0 26 1280 19611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01918733
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218407
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.98925469
X-RAY DIFFRACTIONr_angle_other_deg0.863342672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.40352516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.69825.104670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.068153174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6091596
X-RAY DIFFRACTIONr_chiral_restr0.0760.23087
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02120979
X-RAY DIFFRACTIONr_gen_planes_other0.020.023373
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_it1.2792.42710040
X-RAY DIFFRACTIONr_mcbond_other1.2792.42710039
X-RAY DIFFRACTIONr_mcangle_it2.1383.63212564
X-RAY DIFFRACTIONr_mcangle_other2.1383.63212565
X-RAY DIFFRACTIONr_scbond_it1.4532.6178693
X-RAY DIFFRACTIONr_scbond_other1.4532.6168690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4033.83312904
X-RAY DIFFRACTIONr_long_range_B_refined4.75330.1920784
X-RAY DIFFRACTIONr_long_range_B_other4.68729.87920558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 420 -
Rwork0.253 8427 -
obs--93.31 %
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)
12.03470.07460.21612.0419-1.13131.37320.0444-0.1556-0.01380.13120.00330.0156-0.1623-0.0052-0.04770.1118-0.0212-0.01430.1061-0.03210.0208-0.1351-12.055751.4842
20.5754-0.08720.66730.2786-0.124620.02190.0029-0.071-0.03160.01940.01280.15380.2114-0.04130.0967-0.025-0.01260.1011-0.01950.0427-1.7041-28.826348.1891
34.6605-1.17110.91061.6454-1.14063.39920.03050.3297-0.2135-0.1530.03920.03240.1329-0.0629-0.06970.1212-0.0468-0.02230.0805-0.03630.0386-15.1916-32.421929.796
41.9453-0.5047-0.97872.44921.21533.02720.03850.0223-0.2265-0.0420.0601-0.2261-0.01570.0163-0.09860.0533-0.02620.00420.035-0.0240.0717-0.9335-22.647435.423
51.00390.24750.09041.02540.84522.03670.021-0.0664-0.2029-0.07230.02720.06390.11420.0109-0.04830.098-0.0289-0.02350.05580.00070.0747-12.2455-36.091246.2245
61.50540.0041-0.44631.0684-0.7251.1143-0.00850.05020.08150.0258-0.0071-0.0096-0.0093-0.00790.01560.0737-0.0169-0.01670.0581-0.02350.02761.2198-7.613829.0299
70.9874-0.268-0.45640.83960.22550.421-0.00850.01310.12280.0006-0.0506-0.0933-0.07020.05630.05910.1286-0.0265-0.02670.10010.00810.12274.11396.631331.8523
82.7038-0.0328-1.60791.6683-1.02333.08070.0354-0.20080.2860.2930.0326-0.0016-0.2409-0.0716-0.06790.2023-0.0157-0.00520.0955-0.08370.0846-1.721614.376251.6056
90.7834-0.4093-0.05421.130.09520.93630.0609-0.05360.19810.118-0.0238-0.0333-0.0687-0.0519-0.03710.109-0.0252-0.01190.0598-0.03030.09121.411911.729737.8798
101.4680.3763-0.42981.2075-0.50960.7690.01630.01650.04220.01260.0150.0598-0.02510.0185-0.03130.0697-0.0146-0.01270.0399-0.02050.02251.615815.8148-23.6707
110.98130.0567-0.22260.55310.22410.5418-0.00540.06760.07250.00230.0110.0112-0.04150.0414-0.00560.0512-0.0069-0.02160.0202-0.00590.03333.943429.5578-19.5221
124.5245-0.6042-1.45941.0719-0.84693.1938-0.1001-0.40360.18120.27920.0696-0.1093-0.11020.13140.03050.1959-0.0021-0.01560.0746-0.06170.0662-1.361934.14931.1475
131.67650.10381.76620.9561-0.6392.5068-0.14330.09930.0884-0.02960.0944-0.0586-0.14960.11830.04880.19150.0006-0.00120.2013-0.10210.20225.148519.683-7.7998
141.4621-0.25980.31030.7880.03571.08020.0633-0.00790.24990.1039-0.03760.1038-0.0702-0.1286-0.02570.1101-0.01270.00460.0544-0.0090.11290.23738.4053-15.3823
150.51710.1275-0.121.614-0.14771.13890.0052-0.03040.00320.03640.0362-0.01520.05960.0635-0.04140.05310.0026-0.00820.0267-0.01470.00931.0224.2344-3.516
160.5099-0.1330.10310.38430.03110.5512-0.045-0.0537-0.03610.02810.0383-0.01880.12090.02510.00670.0945-0.00920.00060.0279-0.01530.0496-4.4321-8.8202-7.1761
173.8074-1.83822.1371.8535-2.42843.5028-0.03440.187-0.277-0.10370.02630.10510.1208-0.02040.00810.092-0.0479-0.01480.0465-0.01090.1012-15.7511-9.3024-25.9495
180.09060.4562-0.05992.4749-0.42221.942-0.01180.0253-0.0622-0.05860.0511-0.17820.00760.065-0.03930.1112-0.0279-0.00790.0967-0.05980.148-1.9281-1.1124-20.2461
191.27250.0570.11690.58070.22891.45790.0541-0.0426-0.1176-0.05190.01420.12120.0994-0.0847-0.06820.112-0.02820.01840.01160.00310.0769-12.735-14.5048-10.1279
201.99030.25670.63970.25260.01741.1704-0.06670.10540.1018-0.03020.0664-0.056-0.09360.06050.00030.0254-0.00790.00060.0238-0.01810.035734.389524.7845-20.1825
211.1005-0.3519-0.11810.71440.16980.2595-0.0470.1829-0.1464-0.0309-0.01510.03020.0508-0.10520.06210.0642-0.01350.00050.0868-0.05380.052431.094811.8592-27.4338
224.7835-1.66330.3061.2376-1.17433.4182-0.13520.0103-0.5940.10510.00530.32710.24650.07690.12990.15050.00650.06710.01040.02280.196437.4547-6.7653-17.7631
231.9213-0.4886-1.43291.0262-0.0472.2351-0.0247-0.1048-0.28460.0685-0.0669-0.06730.02410.20640.09170.0698-0.0078-0.0060.04480.00480.102335.87739.3881-16.6705
241.1843-1.47520.23332.1063-0.54881.65380.08450.1991-0.3706-0.1242-0.1210.25720.1401-0.01460.03650.1773-0.0086-0.01030.1702-0.12870.292932.78530.7891-32.4729
252.97780.2638-0.49381.7980.26112.6481-0.0221-0.1653-0.01330.14620.02890.02140.2304-0.0022-0.00690.03120.00250.00360.02450.00920.006836.003612.834-0.2316
261.45990.7418-0.40331.1835-0.55770.68760.1269-0.29430.15220.2232-0.02190.0941-0.0253-0.0014-0.1050.0955-0.02940.02010.1221-0.04740.036438.023128.07527.4581
274.654-0.3446-1.05881.3-0.07153.6990.05250.03550.64520.1625-0.1433-0.075-0.29780.02260.09080.0851-0.02910.00780.0604-0.04550.174950.466644.0436-3.0746
281.62730.56610.21511.3802-0.16271.15120.1512-0.41320.22530.1755-0.10740.0572-0.0870.0071-0.04380.1033-0.03150.02940.1382-0.0890.064245.094534.03627.122
292.8802-0.076-0.72781.43010.88171.79240.0545-0.28970.10620.16420.00870.13660.0630.0486-0.06320.0849-0.00210.01980.1289-0.02650.034434.8373-5.171456.2419
301.69121.0675-1.00541.5604-1.03211.42290.1528-0.27830.2290.3305-0.10260.1632-0.1221-0.0659-0.05010.151-0.0370.04760.2116-0.12430.081241.46548.252760.7906
315.44350.2661-0.23342.17970.16352.1905-0.03090.03490.59160.0402-0.04580.1097-0.1037-0.04460.07670.0911-0.00670.01850.0618-0.04620.112150.711421.397247.0141
321.7555-1.01862.41082.4335-1.50574.5176-0.0569-0.27790.19690.22370.02290.2638-0.1079-0.29290.03410.03770.00250.03350.0998-0.0970.151736.514510.0646.115
331.55891.32120.05371.9725-0.31051.01110.2278-0.29140.22590.2342-0.1791-0.0017-0.16290.0208-0.04860.2221-0.04340.06010.2198-0.13340.127648.486814.761462.6028
342.7708-0.17211.05631.00370.63791.7189-0.0102-0.03520.1199-0.0010.02970.0608-0.0618-0.0014-0.01950.0106-0.01350.00520.03110.00550.032234.18931.459632.1157
350.8838-0.46610.20211.05170.15680.20830.02940.1088-0.0809-0.04850.0489-0.00210.0139-0.013-0.07830.072-0.015-0.02380.1537-0.01250.064431.4221-11.904526.3817
364.4659-1.4653-0.03951.9475-1.17322.45660.0431-0.196-0.29410.07090.03460.15710.1015-0.0128-0.07770.1144-0.0096-0.03830.0593-0.02060.059737.0565-29.047138.7573
370.57120.36920.54551.72080.45290.9278-0.06370.1153-0.0437-0.05690.14930.40170.0627-0.0696-0.08560.1194-0.03180.00770.15320.03210.196530.2441-12.843741.4904
380.8877-0.5337-0.38541.7426-0.76121.29230.13230.116-0.1991-0.1761-0.0898-0.02160.10130.0526-0.04250.17670.0022-0.05010.1913-0.06650.180735.269-21.363323.5816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 60
2X-RAY DIFFRACTION2A61 - 167
3X-RAY DIFFRACTION3A168 - 207
4X-RAY DIFFRACTION4A208 - 235
5X-RAY DIFFRACTION5A236 - 311
6X-RAY DIFFRACTION6B-1 - 89
7X-RAY DIFFRACTION7B90 - 167
8X-RAY DIFFRACTION8B168 - 204
9X-RAY DIFFRACTION9B205 - 311
10X-RAY DIFFRACTION10C-1 - 90
11X-RAY DIFFRACTION11C91 - 167
12X-RAY DIFFRACTION12C168 - 207
13X-RAY DIFFRACTION13C208 - 235
14X-RAY DIFFRACTION14C236 - 311
15X-RAY DIFFRACTION15D0 - 90
16X-RAY DIFFRACTION16D91 - 167
17X-RAY DIFFRACTION17D168 - 204
18X-RAY DIFFRACTION18D205 - 235
19X-RAY DIFFRACTION19D236 - 311
20X-RAY DIFFRACTION20E0 - 87
21X-RAY DIFFRACTION21E88 - 167
22X-RAY DIFFRACTION22E168 - 204
23X-RAY DIFFRACTION23E205 - 248
24X-RAY DIFFRACTION24E249 - 311
25X-RAY DIFFRACTION25F-2 - 60
26X-RAY DIFFRACTION26F61 - 172
27X-RAY DIFFRACTION27F173 - 205
28X-RAY DIFFRACTION28F206 - 311
29X-RAY DIFFRACTION29G-1 - 98
30X-RAY DIFFRACTION30G99 - 167
31X-RAY DIFFRACTION31G168 - 207
32X-RAY DIFFRACTION32G208 - 235
33X-RAY DIFFRACTION33G236 - 311
34X-RAY DIFFRACTION34H-1 - 89
35X-RAY DIFFRACTION35H90 - 167
36X-RAY DIFFRACTION36H168 - 206
37X-RAY DIFFRACTION37H207 - 235
38X-RAY DIFFRACTION38H236 - 311

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