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- PDB-3uv7: Ec_IspH in complex with buta-2,3-dienyl diphosphate (1300) -

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Open data


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Basic information

Entry
Database: PDB / ID: 3uv7
TitleEc_IspH in complex with buta-2,3-dienyl diphosphate (1300)
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / iron-sulfur protein / IspH / LytB / isoprenoid biosynthesis / non-mevalonate pathway
Function / homology
Function and homology information


hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
4-hydroxy-3-methylbut-2-enyl diphosphate reductase / LytB protein / 4-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
Similarity search - Domain/homology
buta-2,3-dien-1-yl trihydrogen diphosphate / IRON/SULFUR CLUSTER / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSpan, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / Schulz, C. / Oldfield, E. / Groll, M.
CitationJournal: Nat Commun / Year: 2012
Title: Discovery of acetylene hydratase activity of the iron-sulphur protein IspH.
Authors: Span, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / Li, K. / Schulz, C. / Oldfield, E. / Groll, M.
History
DepositionNov 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)72,7446
Polymers71,5812
Non-polymers1,1634
Water8,557475
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3723
Polymers35,7911
Non-polymers5822
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)36,3723
Polymers35,7911
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.400, 80.510, 111.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99971, 0.009932, 0.021949), (0.010109, 0.999917, 0.007966), (-0.021868, 0.008186, -0.999727)-65.94643, 0.31014, -0.46057

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Components

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


Mass: 35790.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ispH, lytB, yaaE, b0029, JW0027 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: P62623, EC: 1.17.1.2
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-0CN / buta-2,3-dien-1-yl trihydrogen diphosphate


Mass: 230.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS, 0.2 M ammonia 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: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2011
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 84324 / Num. obs: 84071 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.3
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8
Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.283 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20966 4204 5 %RANDOM
Rwork0.15964 ---
all0.17 84071 --
obs0.16214 79867 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.911 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---1.5 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 42 475 5290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194893
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210
X-RAY DIFFRACTIONr_angle_refined_deg2.3561.9766642
X-RAY DIFFRACTIONr_angle_other_deg0.5652.10620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68624.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93215853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0321544
X-RAY DIFFRACTIONr_chiral_restr0.2220.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024
X-RAY DIFFRACTIONr_rigid_bond_restr8.15934891
X-RAY DIFFRACTIONr_sphericity_free13.9555119
X-RAY DIFFRACTIONr_sphericity_bonded8.92755171
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 286 -
Rwork0.165 5476 -
obs--99.88 %
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)
13.8972-0.7456-0.43910.3420.35150.43390.0032-0.0468-0.1015-0.03250.0209-0.0095-0.00320.0142-0.0240.069-0.00520.01020.04-0.0020.0557-13.245-6.4167-9.1902
22.30090.22591.07660.6981-0.01950.52750.1442-0.1023-0.1403-0.0562-0.0735-0.01070.0806-0.0329-0.07060.06120.0005-0.01340.0671-0.00720.0349-29.79-10.2178-10.8744
33.3553-0.4767-0.63640.11360.17840.3920.27940.3915-0.15480.0049-0.119-0.02370.0639-0.0946-0.16050.08110.0053-0.08620.1621-0.03560.1319-40.1233-13.3986-21.8586
44.7594-0.89290.1540.94890.45470.30550.03360.0477-0.2255-0.04890.0050.005-0.02620.0179-0.03860.0660.0195-0.00180.0579-0.02310.0402-26.6997-10.15-21.5677
52.5281-2.57461.10383.1321-0.66260.91110.11810.30660.0359-0.1441-0.1822-0.010.01930.2240.06410.05820.0242-0.03690.1223-0.03620.0542-37.245-9.4638-27.6925
60.28180.23380.59390.20140.49221.26380.0269-0.03040.01650.0046-0.04730.02870.0461-0.0590.02040.06670.0305-0.03240.0912-0.03350.0585-41.1127-4.7034-20.7621
71.812.6229-0.20525.71111.18781.1857-0.05490.01150.2511-0.20940.00830.499-0.0892-0.010.04660.04240.0387-0.06570.0789-0.02070.1655-48.4445-0.2186-22.7784
80.3244-0.23410.15560.1972-0.2250.5903-0.00790.0113-0.01770.01870.00550.0158-0.0006-0.03480.00230.05730.00540.00280.0745-0.0130.0433-39.0981-0.5802-11.761
91.887-1.6414-0.25723.6557-0.79580.71720.1013-0.06530.09960.22710.01110.3331-0.07070.013-0.11250.09490.0040.08740.0511-0.04390.1463-43.877615.3877-8.9363
100.6677-0.8172-0.48391.34840.54660.35950.03460.01230.0358-0.13880.00020.0527-0.0191-0.0194-0.03480.0760.0216-0.01390.0502-0.00230.0469-31.098811.9935-17.2433
110.61350.23510.01631.04850.00490.56270.02780.09790.0714-0.0967-0.04230.125-0.1204-0.04680.01450.06250.038-0.00980.03580.00780.0529-34.616720.9327-16.2468
120.2510.19960.19171.66630.02340.16430.00670.0155-0.00520.0288-0.01-0.0704-0.01540.00110.00330.06550.01620.01120.0453-0.010.0407-24.212514.3054-10.0519
130.8932-0.4630.52611.4706-0.74890.49420.0545-0.0050.07030.0938-0.01760.1645-0.01590.0057-0.03690.10490.01250.02860.0335-0.02050.0486-29.333322.7816-5.3308
140.4116-0.0789-0.24690.17770.11060.17520.0437-0.02150.02550.0262-0.0279-0.0202-0.0041-0.0014-0.01580.05840.0028-0.00240.0643-0.00730.0395-19.41382.8805-5.6315
150.61750.13020.14220.40720.31480.34570.00090.00920.0225-0.04770.0053-0.0908-0.0128-0.0225-0.00620.04450.00380.01810.0481-0.0020.0708-11.48850.4282-15.5779
161.08770.3864-0.1940.82270.42661.5958-0.01590.0508-0.1097-0.12280.058-0.18080.06420.1381-0.04220.04060.01530.03410.0489-0.01270.0868-2.5566-8.451-20.4515
171.2646-0.0248-0.0030.40420.18020.08380.0285-0.0056-0.0192-0.0093-0.0092-0.04920.0086-0.0093-0.01930.06230.00540.00110.0513-0.00430.0465-14.745-11.6566-13.5003
181.6053-1.2538-1.18142.00282.2332.71060.0267-0.113-0.0750.16180.0773-0.12670.2317-0.0081-0.1040.04920.0062-0.01130.0653-0.00920.0863-7.6125-11.8267-7.5263
193.21310.51281.81470.14530.43471.3749-0.0165-0.158-0.11230.0044-0.00280.01450.038-0.06280.01930.0728-0.01520.0070.0747-0.00170.0309-31.7295-7.4455-2.0646
202.0209-2.2779-2.722.8232.25626.7723-0.08110.2206-0.38080.1569-0.29710.45580.0504-0.46350.37820.0695-0.1130.00590.2118-0.0240.1019-44.1731-13.8184-8.02
213.45881.1096-0.76510.823-0.35770.5374-0.09630.0608-0.02570.05120.070.1516-0.00480.00270.02630.05380.010.01930.01680.00380.1056-52.5357-6.31579.8524
220.6491-0.33450.26370.6013-0.31040.23820.0380.0155-0.01320.0304-0.00910.02090.0575-0.0011-0.02890.0772-0.0065-0.00780.04640.00570.0286-33.6619-11.247817.9403
236.672-1.3385-0.692.6393-2.30942.59980.00250.0406-0.0932-0.03810.05410.07230.044-0.076-0.05670.0841-0.025-0.0430.04410.01790.0397-33.6927-18.086525.5336
240.20860.18420.20220.17180.18550.20460.02210.01140.00170.0375-0.0047-0.01520.04410.0136-0.01730.07240.0021-0.02940.06850.00090.0447-24.8297-6.051724.9947
250.403-0.4262-0.14993.9017-2.27751.7791-0.00850.04270.04520.0797-0.1793-0.3184-0.05820.08290.18780.0376-0.0236-0.04710.06240.01520.0846-18.2292.037220.8728
260.2051-0.08510.38440.4429-0.16890.73910.00750.0340.0083-0.0612-0.007-0.0920.04140.0496-0.00040.05260.0048-0.00850.07510.00090.0446-23.1874-4.247115.8769
271.06710.0235-0.46914.55931.38030.63120.13190.05150.2467-0.18080.0588-0.2748-0.1076-0.0108-0.19070.0492-0.01790.02840.05520.02550.12-23.571812.26019.0162
280.45840.819-0.49382.6454-0.72830.55250.0146-0.01430.01280.13530.0167-0.1324-0.00170.0181-0.03120.0675-0.0151-0.0090.0471-0.00790.0435-32.941313.292316.8469
291.42490.983-1.07062.7596-0.06031.0310.0161-0.1820.03530.02310.0414-0.12220.00570.1805-0.05760.0469-0.0326-0.02770.0603-0.01040.1146-23.621114.997117.96
300.48110.00130.16491.18130.00070.38680.0191-0.00610.05440.0436-0.00660.0133-0.04780.0054-0.01250.0602-0.01450.0190.02840.00150.0497-37.490619.806313.6053
311.39310.04450.28171.42971.10240.89420.07350.02080.1071-0.0879-0.0006-0.1208-0.05080.0024-0.07280.1006-0.00520.02160.0240.02280.0398-36.110122.86545.5501
320.49240.3299-0.13030.84760.38580.3923-0.00940.02320.0364-0.03020.00610.0453-0.0128-0.00890.00330.05760.0002-0.00710.05590.0140.047-44.20923.2456.1799
335.78461.1015-3.88452.1171-3.74817.53310.33210.0890.0436-0.0471-0.02250.3144-0.04630.048-0.30960.02590.0027-0.01240.03320.02740.2703-60.53580.26648.1165
340.808-0.03650.19150.4552-0.39310.39120.04180.00390.0470.1054-0.0050.0957-0.06760.0304-0.03680.06840.00420.04460.05130.01890.0879-49.29650.422417.5194
350.5218-0.8348-0.30032.05790.47140.17430.0018-0.01610.00110.2247-0.00530.2246-0.00420.00860.00350.0722-0.01290.06310.0178-0.00080.1116-56.6758-0.349218.351
363.531-2.90453.23473.847-2.07824.4115-0.1342-0.0295-0.10480.5722-0.01370.72280.3653-0.23410.1480.2271-0.05840.20380.0316-0.01370.2812-64.1025-8.153621.2283
370.9493-0.1043-0.02260.86510.1390.0293-0.0330.0552-0.03590.10060.02740.14940.01220.01810.00560.0421-0.01410.01730.0481-0.00830.0963-50.9984-11.458714.0305
381.94860.5938-2.51272.7331-2.28784.1762-0.02970.086-0.2502-0.2095-0.02020.39310.1513-0.02820.04990.0284-0.0264-0.02520.107-0.02370.1274-58.0796-11.68488.082
392.8587-0.63511.21970.3112-0.63241.3253-0.08470.1428-0.049-0.02380.0014-0.02670.07880.04350.08320.06150.01480.01130.08950.00550.0391-33.1177-7.8043.1291
407.88582.60770.119133.885-5.02664.2482-0.08860.51180.0936-0.4742-0.517-1.12341.33860.33060.60560.47330.08390.17070.06710.05540.0943-22.6891-15.87717.9383
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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