[English] 日本語
Yorodumi
- PDB-3o1k: Crystal structure of putative dihydroneopterin aldolase (FolB) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o1k
TitleCrystal structure of putative dihydroneopterin aldolase (FolB) from Vibrio cholerae O1 biovar El Tor str. N16961
ComponentsDihydroneopterin aldolase FolB, putative
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / clan THBO-biosyn (CL0334) / (PF02152) / dihydroneopterin aldolase / FolB / folic acid and derivative metabolic process (GO:0006760)
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid-containing compound metabolic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2o90 / Resolution: 1.95 Å
AuthorsNocek, B. / Zhou, M. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of putative dihydroneopterin aldolase (FolB) from Vibrio cholerae O1 biovar El Tor str. N16961
Authors: Nocek, B. / Zhou, M. / Papazisi, L. / Anderson, W. / Joachimiak, A.
History
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydroneopterin aldolase FolB, putative
B: Dihydroneopterin aldolase FolB, putative
C: Dihydroneopterin aldolase FolB, putative
D: Dihydroneopterin aldolase FolB, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5435
Polymers59,4814
Non-polymers621
Water2,432135
1
A: Dihydroneopterin aldolase FolB, putative
B: Dihydroneopterin aldolase FolB, putative
C: Dihydroneopterin aldolase FolB, putative
D: Dihydroneopterin aldolase FolB, putative
hetero molecules

A: Dihydroneopterin aldolase FolB, putative
B: Dihydroneopterin aldolase FolB, putative
C: Dihydroneopterin aldolase FolB, putative
D: Dihydroneopterin aldolase FolB, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,08610
Polymers118,9618
Non-polymers1242
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area20950 Å2
ΔGint-81 kcal/mol
Surface area38850 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-28 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.098, 101.734, 116.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Dihydroneopterin aldolase FolB, putative


Mass: 14870.187 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9KUJ6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% isopropanon, 0.1 M Hepes, 10%Peg 4K, 25 % sucrose as cryo protectant, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 41310 / Num. obs: 41277 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 30
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Num. unique all: 2045 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: 2o90 / Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.444 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24619 2069 5 %RANDOM
Rwork0.19413 ---
all0.2 41150 --
obs0.19689 39077 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.428 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--2.04 Å20 Å2
3----3.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 4 135 3867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223804
X-RAY DIFFRACTIONr_bond_other_d0.0010.022572
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9625147
X-RAY DIFFRACTIONr_angle_other_deg1.02336281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9695471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18524.475181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9115701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5671532
X-RAY DIFFRACTIONr_chiral_restr0.1230.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
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_it1.1531.52352
X-RAY DIFFRACTIONr_mcbond_other0.3531.5955
X-RAY DIFFRACTIONr_mcangle_it2.03623795
X-RAY DIFFRACTIONr_scbond_it3.23931452
X-RAY DIFFRACTIONr_scangle_it5.4164.51351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 150 -
Rwork0.274 2782 -
obs--96.7 %
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)
16.24940.24876.05930.84891.526610.3318-0.19530.23630.2691-0.099-0.09290.0385-0.33880.2750.28820.18470.0114-0.00550.21480.00890.173624.003241.0737.3297
27.56223.03013.49751.7608-0.00554.04220.0799-0.0872-0.00080.052-0.13260.0094-0.01250.20170.05280.1550.04510.0190.316-0.01990.141841.039342.85450.3892
315.8754.8977-5.923317.6397-4.62414.72860.2768-0.39430.0712-0.0011-0.4173-0.5749-0.6880.78350.14050.0546-0.0312-0.01520.60390.03510.032852.961647.985853.9672
412.9143-0.81584.68460.3531.70157.74250.2395-0.66430.04390.01280.1191-0.08020.28010.0911-0.35860.18840.0132-0.01360.314-0.02650.153841.200144.006852.8169
53.30091.82022.76551.90421.02723.7526-0.08150.1888-0.095-0.11390.0609-0.0145-0.14370.32240.02060.17490.03560.01670.205-0.00990.142226.579739.082536.3671
61.5885-2.99970.04075.8496-1.92434.8767-0.20490.059-0.00240.04510.1389-0.08560.31290.01660.06610.3193-0.03260.00050.2871-0.0760.163616.992527.600632.3659
73.85795.0663-3.38475.2194-4.56142.39010.3009-0.3097-0.28780.2862-0.4619-0.257-0.14450.31740.1610.44980.1388-0.09670.295-0.11020.143225.859129.125837.0779
826.91846.96185.92.5070.21541.8332-0.12490.0141-0.6025-0.4722-0.0284-0.42610.46230.07210.15330.51890.21370.10210.2986-0.01450.112837.178432.248843.6023
92.31526.7939-5.603914.0879-13.655715.65040.277-0.0169-0.95090.0832-0.3739-1.33790.57950.96780.09690.23590.2779-0.25180.5498-0.03740.62146.811136.573947.6736
103.25130.9558-2.58290.347-1.21752.10550.1732-0.0957-0.0849-0.0365-0.2797-0.065-0.03050.37120.10650.150.01980.0190.359-0.00310.149945.769445.002941.2169
116.92516.84045.029513.23816.908323.67760.02710.31830.0783-0.1185-0.3027-0.43770.35570.67830.27570.11890.06970.03450.3192-0.03940.149338.628537.78234.6918
126.5305-5.41990.286919.2662-0.26011.7042-0.244-0.3111-0.2865-0.60050.58150.31040.74150.0238-0.33750.3970.0696-0.0760.3314-0.07290.136135.096233.40332.198
133.22753.49546.58193.85756.773316.596-0.08960.06690.1282-0.0903-0.01380.0622-0.01150.14140.10340.16850.00690.00060.26690.02550.165734.088447.031941.0121
143.3222-0.54873.27543.76623.57477.6604-0.0139-0.0901-0.07810.0540.1685-0.06210.07280.21-0.15460.2253-0.02920.01640.33560.06040.117938.468556.492952.8455
154.29813.67450.64816.99647.806713.292-0.29930.3406-0.13-0.06930.2437-0.13490.21040.37210.05570.1695-0.01040.03170.43220.0540.120936.17346.409633.0132
167.1031-2.2359-5.39424.0541.54698.4373-0.15520.7415-0.2073-0.5387-0.24880.18910.5118-0.33670.4040.3803-0.05310.00120.26150.0240.139223.563667.605534.9298
1715.21913.769-8.43441.3171-2.71847.0439-0.0783-0.0762-0.23240.0637-0.0735-0.0135-0.08170.11560.15180.2246-0.006-0.01830.1514-0.0210.159111.894363.640552.1936
189.2623-0.8-4.453811.64252.31049.2766-0.3247-0.25480.1168-0.33810.22740.64490.5959-0.78490.09730.1873-0.0489-0.00790.36810.02030.1424-7.628955.563153.5468
199.92151.6847-5.16960.2986-1.84148.83380.0697-0.2179-0.11580.01340.0308-0.0161-0.0364-0.2571-0.10050.20880.0069-0.01240.17220.00570.18921.997258.763555.9184
204.04983.5606-2.49065.491-3.02753.7171-0.00530.09760.1148-0.09130.06090.1093-0.0656-0.058-0.05560.2306-0.0183-0.02540.15410.0050.158817.543868.904341.524
21-0.80020.72170.773417.986314.55718.6117-0.06980.1126-0.01490.4835-0.34070.4206-0.81120.57670.41050.4421-0.23040.03140.20490.05990.181428.185681.398640.6961
229.43874.2568-1.3672.70430.88280.51930.2063-0.27490.4591-0.0344-0.23260.1425-0.1366-0.15780.02630.4589-0.106-0.05920.11640.0520.233719.182779.00245.4821
2321.19346.0613-0.87085.028-0.60651.73990.0081-0.13630.59750.1210.00420.283-0.7283-0.0145-0.01230.31250.0179-0.00280.1133-0.01930.18417.459973.304750.3257
2424.06227.28872.538313.16914.91866.6250.6794-0.63071.09770.6268-0.56080.5142-0.29-1.0524-0.11860.30640.05090.09330.2367-0.06850.1974-2.299667.626252.8127
256.5490.2254-2.20550.2522.06445.68780.0877-0.199-0.08720.0421-0.15010.01160.1565-0.34320.06250.19610.0033-0.01780.27210.00880.2427-2.702159.289245.5125
266.13254.6089-0.68613.698-1.27981.049-0.0796-0.02890.31810.1630.1150.2205-0.3043-0.285-0.03540.24220.0706-0.01680.24870.00850.20131.941866.904641.6682
275.5158-0.8175-2.82698.0547-0.92667.11330.01760.07650.31740.142-0.11830.1524-0.49280.09730.10070.34530.0281-0.03320.0670.05480.21448.565375.31739.929
283.02363.2147-4.40487.2667-7.94599.6616-0.13780.0862-0.0373-0.1047-0.0657-0.0877-0.0594-0.0150.20340.2356-0.03-0.04420.1654-0.00240.163911.987662.805640.2876
290.6244-1.00270.70487.373-2.81311.20290.0256-0.1051-0.02540.23450.07860.3684-0.077-0.0452-0.10410.21290.00430.00910.2289-0.00390.20094.506247.878752.4525
301.0481.0113-1.29039.7006-9.898111.2852-0.07020.15720.14070.3398-0.0394-0.0097-0.34280.14110.10960.2179-0.0064-0.04120.1716-0.02070.17788.513459.58239.5303
310.418-2.3547-1.68348.888710.063827.21960.0850.0204-0.0385-0.2698-0.0490.226-0.1811-0.3166-0.0360.1497-0.0453-0.01750.34040.09510.1735.56855.639739.7278
322.1314-2.848-0.045616.99910.93878.3039-0.0272-0.13310.03430.03020.025-0.0638-0.0156-0.05130.00220.2338-0.09920.01220.3050.02610.105733.305267.347655.3712
3320.0229-6.90041.727822.0426-0.688923.16740.2092-0.10331.116-0.1487-0.62870.2776-1.1837-1.61640.41950.525-0.06250.06290.244-0.04490.101125.626581.77757.9437
340.587-1.2026-4.24421.65756.439120.90360.27260.02720.0218-0.27130.0019-0.1259-0.8122-0.2185-0.27450.4135-0.0894-0.04180.25280.02280.178729.770272.52558.9616
356.0367-2.356-8.46211.58953.410214.5295-0.05940.0586-0.05180.0566-0.054-0.1195-0.0268-0.05770.11340.1921-0.02290.00560.24040.05350.147433.500861.854344.1519
368.7758-0.95810.64841.2723-0.78710.1344-0.0450.42540.15210.11480.0116-0.0684-0.05620.06860.03340.21570.02940.05190.4229-0.00480.096644.496851.898133.6081
376.5257-3.3029-2.441712.2258-6.64576.67420.0331-0.29130.22680.0038-0.1904-0.4447-0.02420.49380.15730.095-0.00110.05620.4685-0.0050.064750.286751.911738.1552
386.1578-10.999-3.085518.80365.47437.7547-0.1127-0.05260.21130.16220.0879-0.32730.1230.94190.02490.1555-0.07520.00050.40040.05550.126343.964364.249648.4906
396.0572-7.38950.126516.0555-1.76540.619-0.5404-1.04060.9430.72580.353-1.1687-0.57840.42210.18740.5616-0.1876-0.22440.4344-0.14340.243937.515176.510152.7893
40-0.24423.80672.518718.439611.49795.7441-0.0205-0.1607-0.0445-0.184-0.0041-0.1623-0.3011-0.14580.02460.95830.0476-0.19120.2210.05050.120728.611778.064647.4555
419.1051-5.8339-3.70155.53653.84752.1755-0.38060.220.5181-0.15640.17630.0861-0.20.24960.20430.3253-0.2598-0.12510.40330.22020.254536.861472.111141.3985
4220.65713.48379.02177.9994-0.91575.1652-0.01910.2036-0.2404-0.121-0.0528-0.4962-0.23440.98860.07190.1768-0.17120.12350.67370.07590.13943.763467.260837.7347
437.1911-3.4649-10.01281.73385.074418.8827-0.11040.06390.0598-0.0298-0.08330.089-0.08360.0790.19370.232-0.0185-0.00490.20120.01680.173428.967165.217644.0289
443.07752.3419-3.61992.7273-2.46263.98360.0758-0.21120.02360.2443-0.0544-0.0515-0.05940.2674-0.02140.2456-0.0276-0.03140.23550.00770.157117.605267.76454.7419
456.4062-2.1599-4.53422.3250.831810.89310.08430.18810.2531-0.2653-0.0768-0.1252-0.45040.311-0.00740.2621-0.0581-0.00220.21020.05140.145830.818168.445536.5901
460.5806-0.43312.02399.1192-8.464311.8977-0.10040.12370.0374-0.2541-0.243-0.3218-0.01950.56160.34340.19250.0124-0.00430.2091-0.01180.18799.313453.331138.1242
472.5266-4.31790.40866.69-0.29312.5515-0.0104-0.03530.04090.04350.0337-0.03180.25790.085-0.02330.23050.0252-0.02030.1876-0.01060.202112.13234.577449.3348
4844.8144-16.3699-30.159810.948827.22722.7662-2.2030.5073-4.88073.00251.808-0.6832.64952.90790.3951.0572-0.0393-0.61921.45380.25210.993621.036921.81348.008
492.3389-0.4037-0.88516.4971-1.5345.6796-0.0330.05710.00540.2977-0.00690.07420.79010.40460.03980.35580.0931-0.03910.1701-0.02350.131614.755427.261151.2534
506.267-8.16598.139314.7012-15.70619.44760.06880.1104-0.13170.0043-0.05710.1209-0.02510.0451-0.01180.17490.01960.0170.2029-0.02790.155212.504943.876243.0202
511.0562-1.22190.38511.66791.05773.21390.01030.0093-0.0245-0.1772-0.0590.0265-0.2772-0.13910.04870.23420.0284-0.03230.21320.02390.20561.661955.799134.784
524.132-1.74580.54718.81194.25454.020.0982-0.1257-0.0757-0.077-0.16180.2436-0.0748-0.45610.06360.13990.0448-0.07090.28120.01040.1692-5.733256.567238.8207
538.2052-8.8509-3.465916.4525-1.87675.0992-0.11430.24020.05940.17610.3690.2012-0.0187-0.5847-0.25470.19110.0175-0.00780.27820.01780.1695-0.574144.073744.3492
546.9948-3.57175.574511.4719-3.44834.35410.018-0.2855-0.00870.22570.09020.17340.1595-0.2338-0.10820.3621-0.03950.00190.1843-0.00560.20244.098634.510344.3691
5512.2705-5.0324-0.93876.59256.8448.3069-0.3521-0.228-0.75980.6496-0.02340.55920.7483-0.11120.37550.38840.01540.10170.10170.08780.2777.423427.136845.3811
560.831-2.64531.84247.1049-0.07158.96580.05580.0642-0.1045-0.02430.05790.34760.44310.5227-0.11370.26730.06870.00160.2364-0.02420.150115.514629.406739.2619
577.3712-3.21360.45051.8386-1.04771.5301-0.04870.0562-0.1277-0.03410.08650.0350.2061-0.2131-0.03780.2387-0.0054-0.0390.1858-0.01450.17084.705137.930834.654
5811.5182-2.16826.00351.8599-0.92585.703-0.15950.24620.20730.06920.04610.0022-0.1430.35870.11340.19570.0229-0.00780.1779-0.00620.16839.606846.591832.6866
594.5951-5.17135.71626.6535-9.512516.7159-0.096-0.07220.1343-0.0060.0496-0.11150.1425-0.15140.04640.19310.0289-0.00070.2295-0.01040.162717.966238.835444.3142
604.7747-0.69744.47290.4746-0.92765.22020.084-0.0251-0.15310.0014-0.00230.07060.09780.1164-0.08180.1950.02650.01060.2163-0.00890.151620.45738.703140.844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 19
2X-RAY DIFFRACTION2A20 - 29
3X-RAY DIFFRACTION3A30 - 36
4X-RAY DIFFRACTION4A37 - 41
5X-RAY DIFFRACTION5A42 - 50
6X-RAY DIFFRACTION6A51 - 59
7X-RAY DIFFRACTION7A60 - 65
8X-RAY DIFFRACTION8A66 - 75
9X-RAY DIFFRACTION9A76 - 80
10X-RAY DIFFRACTION10A81 - 90
11X-RAY DIFFRACTION11A91 - 96
12X-RAY DIFFRACTION12A97 - 102
13X-RAY DIFFRACTION13A103 - 111
14X-RAY DIFFRACTION14A112 - 121
15X-RAY DIFFRACTION15A122 - 128
16X-RAY DIFFRACTION16B10 - 16
17X-RAY DIFFRACTION17B17 - 25
18X-RAY DIFFRACTION18B26 - 35
19X-RAY DIFFRACTION19B36 - 41
20X-RAY DIFFRACTION20B42 - 50
21X-RAY DIFFRACTION21B51 - 58
22X-RAY DIFFRACTION22B59 - 65
23X-RAY DIFFRACTION23B66 - 75
24X-RAY DIFFRACTION24B76 - 80
25X-RAY DIFFRACTION25B81 - 85
26X-RAY DIFFRACTION26B86 - 94
27X-RAY DIFFRACTION27B95 - 101
28X-RAY DIFFRACTION28B102 - 109
29X-RAY DIFFRACTION29B110 - 117
30X-RAY DIFFRACTION30B118 - 128
31X-RAY DIFFRACTION31C12 - 19
32X-RAY DIFFRACTION32C20 - 26
33X-RAY DIFFRACTION33C27 - 35
34X-RAY DIFFRACTION34C36 - 40
35X-RAY DIFFRACTION35C41 - 47
36X-RAY DIFFRACTION36C48 - 54
37X-RAY DIFFRACTION37C55 - 63
38X-RAY DIFFRACTION38C64 - 74
39X-RAY DIFFRACTION39C75 - 81
40X-RAY DIFFRACTION40C82 - 86
41X-RAY DIFFRACTION41C87 - 96
42X-RAY DIFFRACTION42C97 - 102
43X-RAY DIFFRACTION43C103 - 111
44X-RAY DIFFRACTION44C112 - 121
45X-RAY DIFFRACTION45C122 - 128
46X-RAY DIFFRACTION46D11 - 19
47X-RAY DIFFRACTION47D20 - 28
48X-RAY DIFFRACTION48D29 - 33
49X-RAY DIFFRACTION49D34 - 40
50X-RAY DIFFRACTION50D41 - 45
51X-RAY DIFFRACTION51D46 - 53
52X-RAY DIFFRACTION52D54 - 63
53X-RAY DIFFRACTION53D64 - 70
54X-RAY DIFFRACTION54D71 - 76
55X-RAY DIFFRACTION55D77 - 81
56X-RAY DIFFRACTION56D82 - 87
57X-RAY DIFFRACTION57D88 - 100
58X-RAY DIFFRACTION58D101 - 105
59X-RAY DIFFRACTION59D106 - 111
60X-RAY DIFFRACTION60D112 - 128

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more