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- PDB-4mux: IspH in complex with pyridin-3-ylmethyl diphosphate -

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Basic information

Entry
Database: PDB / ID: 4mux
TitleIspH in complex with pyridin-3-ylmethyl diphosphate
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / Iron-sulfur protein / Reductase / pyridin-3-ylmethyl diphosphate / Cytosol
Function / homology4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain / Rossmann fold - #11270 / Cobalt-precorrin-4 Transmethylase; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / pyridin-3-ylmethyl trihydrogen diphosphate / IRON/SULFUR CLUSTER / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsSpan, I. / Eisenreich, W. / Bacher, A. / Oldfield, E. / Groll, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Insights into the Binding of Pyridines to the Iron-Sulfur Enzyme IspH.
Authors: Span, I. / Wang, K. / Eisenreich, W. / Bacher, A. / Zhang, Y. / Oldfield, E. / Groll, M.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.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_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: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4576
Polymers72,2162
Non-polymers1,2414
Water4,576254
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7293
Polymers36,1081
Non-polymers6212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7293
Polymers36,1081
Non-polymers6212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.780, 80.820, 111.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 4-hydroxy-3-methylbut-2-enyl diphosphate reductase /


Mass: 36107.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: ECDH1ME8569_0026, ispH / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue
References: UniProt: C9QSC3, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-2E4 / pyridin-3-ylmethyl trihydrogen diphosphate


Mass: 269.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS, 0.2 M ammonium sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012
RadiationMonochromator: double-crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 69828 / Num. obs: 66547 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rsym value: 0.052 / Net I/σ(I): 14.44
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 2.38 / Rsym value: 0.574 / % possible all: 95.2

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.7.0029phasing
RefinementResolution: 1.7→10 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.76 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24116 3308 5 %RANDOM
Rwork0.20722 ---
obs0.20892 62840 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å2-0 Å20 Å2
2---2.36 Å2-0 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 48 254 5075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194914
X-RAY DIFFRACTIONr_bond_other_d0.0010.024759
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9786675
X-RAY DIFFRACTIONr_angle_other_deg0.842310922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00924.211228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94215856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6391544
X-RAY DIFFRACTIONr_chiral_restr0.1440.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
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_it1.5052.0242478
X-RAY DIFFRACTIONr_mcbond_other1.5052.0232477
X-RAY DIFFRACTIONr_mcangle_it2.2363.0293095
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3612.3722436
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.702→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 236 -
Rwork0.347 4474 -
obs--95.87 %
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)
15.53520.5267-0.38940.08230.19531.722-0.04330.4937-0.4940.04340.0053-0.05140.3144-0.3250.0380.2576-0.07590.0040.0971-0.03040.1691-27.7999-8.76087.6843
21.4406-1.8376-0.37492.37450.47790.10060.06720.0586-0.1985-0.0136-0.11010.2081-0.01360.0010.04290.323-0.0309-0.05170.12410.01760.1648-5.2539-9.865611.0791
33.85291.8117-1.09570.8626-0.52110.31920.1799-0.4418-0.27280.0876-0.2556-0.1456-0.05250.14690.07580.2542-0.0264-0.11220.26710.11740.11075.001-13.229721.85
42.47651.567-0.15473.3307-0.55550.09980.09490.0723-0.19930.2679-0.05910.0679-0.05140.0126-0.03580.321-0.0553-0.01370.06870.03040.1165-8.1406-9.943221.5563
53.458-0.03791.35066.0229-3.00082.00870.0899-0.83260.01890.6141-0.2883-0.3529-0.2815-0.16750.19840.3846-0.1535-0.09980.25780.04710.05372.4682-9.457827.7062
67.0059-1.57064.03423.2161-3.1784.13030.6473-0.2489-0.44440.1572-0.5556-0.11780.14140.3322-0.09180.2499-0.1022-0.07850.15840.07630.05486.1951-5.14720.7792
710.6759-6.16870.00216.1342-4.56288.0986-0.007-0.27740.90810.025-0.2227-0.6647-0.01640.67010.22970.2851-0.139-0.26380.12930.12240.325813.3478-0.089422.4643
80.1895-0.3472-0.28083.4124-1.10881.48740.09750.07050.0215-0.2017-0.1606-0.1896-0.0285-0.0460.06310.2165-0.0139-0.03090.12090.0420.13613.7894-0.351911.6255
94.2236-1.0465-2.43883.05092.37132.53540.52550.1660.2982-0.1101-0.1301-0.4923-0.2571-0.1481-0.39540.2349-0.0180.10130.08670.14840.38728.916715.05769.178
101.02471.5638-1.67315.7656-3.3712.93070.0801-0.00580.03630.3483-0.0578-0.0888-0.18430.0128-0.02230.2535-0.08390.00010.0817-0.01720.1289-4.156212.232317.3761
111.3762-1.10650.38413.61030.02870.35570.0047-0.07670.07360.3969-0.0702-0.3781-0.17840.01820.06550.36-0.1115-0.06850.0441-0.00810.1734-0.468821.144916.3506
120.5830.0104-0.22342.88151.58360.96380.03160.0370.0771-0.0005-0.05820.1152-0.0263-0.02690.02660.2811-0.04140.03010.0810.00330.1522-10.324114.278310.1974
131.34950.3840.12493.93091.84890.87270.1453-0.03240.0253-0.274-0.0469-0.2185-0.1241-0.0233-0.09840.3111-0.05810.02440.06580.03510.1239-5.688522.7355.1613
140.19210.3506-0.01441.10530.37630.38450.06180.04540.08180.1528-0.01730.08340.0457-0.0415-0.04450.2425-0.01090.00740.12260.01680.1855-15.91842.72125.9717
152.8523-1.23590.28931.0008-0.95961.58890.0198-0.07420.06340.06450.03390.0627-0.0331-0.0381-0.05370.3093-0.04890.09390.0233-0.04830.2031-23.57850.370915.7068
160.09860.05620.32170.2796-0.61254.0519-0.032-0.04530.0572-0.04810.01750.17540.3347-0.34680.01460.3111-0.08230.15610.0864-0.00960.3155-32.5413-8.698920.2866
171.23420.9098-0.59212.04490.08421.45050.08080.0342-0.14280.1544-0.05460.00580.1050.0956-0.02620.2898-0.04030.03780.0394-0.02560.1521-20.2379-11.626213.7127
183.2261.8136-3.17222.7675-4.12396.310.22920.1675-0.1046-0.1933-0.02920.2430.2599-0.0147-0.20.2345-0.0570.03090.0751-0.0580.2299-27.4646-11.69477.9964
197.340.39482.88310.137-0.09211.6714-0.10110.2147-0.1033-0.08380.0114-0.06240.16710.0840.08970.23980.01360.00920.12930.00330.1279-3.2018-7.49592.349
2015.25477.0061-9.24812.4612-6.99696.42610.0857-0.1792-0.4666-0.1458-0.5342-0.7278-0.00780.24480.44850.13220.0673-0.04690.11470.08130.15769.2254-13.56538.0699
214.1626-1.0212-0.12231.3031-0.10720.5056-0.0366-0.2682-0.34840.0312-0.0103-0.25550.14110.09540.04690.23970.0487-0.01530.05810.03910.244723.5213-8.8346-8.0295
221.63330.84630.25430.91560.47980.30520.03870.0183-0.03560.0526-0.0297-0.01990.0909-0.016-0.0090.33230.0377-0.03960.0429-0.01050.1095-1.3312-11.1366-17.6266
238.773-1.7533-0.97641.3281-2.02065.23870.1825-0.0005-0.0607-0.1187-0.01980.09240.24970.1296-0.16280.17550.0387-0.04380.1087-0.02440.0709-1.211-17.7313-25.3743
242.12880.79341.74121.80590.93481.54170.02510.09670.0435-0.0353-0.00560.04430.11640.0475-0.01960.30950.0099-0.04550.0860.00920.0896-10.2399-6.334-24.5956
254.80971.462-1.92313.1713.3696.5082-0.2604-0.26530.1755-0.1227-0.11980.38280.02930.04370.38020.19970.0509-0.08530.03070.0070.215-16.56412.2714-20.4
262.31661.29331.83680.780.92113.02640.0298-0.11480.13150.0897-0.04410.10950.2236-0.0910.01440.23340.0031-0.02660.08210.00680.1228-11.5995-4.1192-15.7344
276.6148-1.2503-2.09514.8445-0.42620.81230.3179-0.38350.4217-0.0638-0.11310.3819-0.08550.1609-0.20480.17570.02680.00720.0767-0.07190.2576-11.131611.8631-8.6596
281.4931-1.163-1.16963.91021.80161.18040.0030.09390.1249-0.2475-0.00690.2531-0.0778-0.0510.00390.28630.0603-0.01750.07110.03690.1222-1.585713.246-16.7888
293.1792-2.1436-0.2716.9603-0.18280.44570.04750.44510.14880.072-0.17080.38160.071-0.16160.12320.19950.0397-0.04590.1267-0.01910.2191-10.948714.9101-18.0527
300.61410.03260.14731.92180.00780.67270.02790.01950.0913-0.0795-0.00440.0673-0.13990.0112-0.02350.29710.03650.02840.02620.01150.15332.170219.7298-13.4637
313.6132-0.85961.87322.042-1.38581.4523-0.02880.02340.19760.17390.02670.1546-0.096-0.00370.00210.30080.04360.03040.0365-0.04430.12021.362422.7644-5.271
320.8564-0.8442-0.15331.1088-0.14210.36190.10790.0217-0.0345-0.0876-0.10320.02370.0010.0472-0.00470.26350.0065-0.01340.10360.00980.14379.37552.9931-6.2736
335.42470.6909-0.19784.32085.71687.79850.759-0.52640.0594-0.299-0.2198-0.399-0.5547-0.174-0.53910.23910.02280.06760.13190.05470.242825.0470.1426-8.0292
343.95340.2466-0.34750.11940.00440.03740.00380.21870.107-0.13960.027-0.1012-0.0334-0.0139-0.03080.33920.03370.07510.0506-0.00670.159714.64680.0242-17.2239
353.60940.5227-0.34421.1103-0.24780.07520.01050.41590.1454-0.3937-0.0828-0.53630.08170.00220.07230.35430.09150.16080.12070.03640.362521.9795-0.0648-17.7379
363.6414-0.21875.1122.94711.93158.91160.32660.1014-0.1652-0.15260.1222-0.39250.37830.2288-0.44880.20730.09390.14020.0784-0.01150.333929.2847-8.6201-20.7933
372.7845-1.54410.44063.1743-0.710.52450.2326-0.033-0.3046-0.3766-0.1213-0.06710.0436-0.016-0.11120.2650.0704-0.02230.0374-0.0150.213715.976-11.5991-13.9576
385.0866-1.6462-4.99894.2924.48417.11490.2378-0.2455-0.35230.2872-0.0702-0.61180.05460.103-0.16760.23380.1069-0.02290.14550.04770.244223.1348-11.765-8.3063
393.3256-1.1760.8240.49670.00251.352-0.09-0.2719-0.01470.0630.04140.00890.2039-0.14770.04860.28160.0174-0.00910.16260.02970.1516-1.8421-7.8341-3.0455
4010.6566-2.9193-3.6157.8436-6.4849.1664-0.1114-0.5501-0.0541-0.22920.19230.13830.33080.1157-0.08090.1611-0.08930.02410.1234-0.0780.1221-12.2489-15.8421-7.5502
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 24
3X-RAY DIFFRACTION3A25 - 37
4X-RAY DIFFRACTION4A38 - 49
5X-RAY DIFFRACTION5A50 - 64
6X-RAY DIFFRACTION6A65 - 77
7X-RAY DIFFRACTION7A78 - 89
8X-RAY DIFFRACTION8A90 - 103
9X-RAY DIFFRACTION9A104 - 114
10X-RAY DIFFRACTION10A115 - 127
11X-RAY DIFFRACTION11A128 - 162
12X-RAY DIFFRACTION12A163 - 181
13X-RAY DIFFRACTION13A182 - 193
14X-RAY DIFFRACTION14A194 - 210
15X-RAY DIFFRACTION15A211 - 246
16X-RAY DIFFRACTION16A247 - 261
17X-RAY DIFFRACTION17A262 - 280
18X-RAY DIFFRACTION18A281 - 297
19X-RAY DIFFRACTION19A298 - 304
20X-RAY DIFFRACTION20A305 - 309
21X-RAY DIFFRACTION21B1 - 7
22X-RAY DIFFRACTION22B8 - 49
23X-RAY DIFFRACTION23B50 - 54
24X-RAY DIFFRACTION24B55 - 76
25X-RAY DIFFRACTION25B77 - 86
26X-RAY DIFFRACTION26B87 - 100
27X-RAY DIFFRACTION27B101 - 112
28X-RAY DIFFRACTION28B113 - 127
29X-RAY DIFFRACTION29B128 - 140
30X-RAY DIFFRACTION30B141 - 181
31X-RAY DIFFRACTION31B182 - 193
32X-RAY DIFFRACTION32B194 - 207
33X-RAY DIFFRACTION33B208 - 216
34X-RAY DIFFRACTION34B217 - 235
35X-RAY DIFFRACTION35B236 - 248
36X-RAY DIFFRACTION36B249 - 261
37X-RAY DIFFRACTION37B262 - 280
38X-RAY DIFFRACTION38B281 - 297
39X-RAY DIFFRACTION39B298 - 305
40X-RAY DIFFRACTION40B306 - 310

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