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- PDB-3tdp: Crystal structure of HSC at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 3tdp
TitleCrystal structure of HSC at pH 4.5
Componentsformate/nitrite transporter
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


transmembrane transporter activity / membrane / metal ion binding
Similarity search - Function
Formate and nitrite transporters signature 1. / Formate/nitrite transporter / Formate/nitrite transporter, conserved site / Formate/nitrite transporter / Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Formate/nitrite transporter
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsCzyzewski, B.K. / Wang, D.-N.
CitationJournal: Nature / Year: 2012
Title: Identification and characterization of a bacterial hydrosulphide ion channel.
Authors: Czyzewski, B.K. / Wang, D.N.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: formate/nitrite transporter
B: formate/nitrite transporter
C: formate/nitrite transporter
D: formate/nitrite transporter
E: formate/nitrite transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,80013
Polymers135,5965
Non-polymers1,2048
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18670 Å2
ΔGint-260 kcal/mol
Surface area40510 Å2
MethodPISA
2
A: formate/nitrite transporter
B: formate/nitrite transporter
C: formate/nitrite transporter
D: formate/nitrite transporter
E: formate/nitrite transporter
hetero molecules

A: formate/nitrite transporter
B: formate/nitrite transporter
C: formate/nitrite transporter
D: formate/nitrite transporter
E: formate/nitrite transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,60026
Polymers271,19210
Non-polymers2,40816
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area41510 Å2
ΔGint-698 kcal/mol
Surface area76830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.515, 162.903, 194.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
formate/nitrite transporter


Mass: 27119.152 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_22300, Putative formate/nitrite transporter / Plasmid: pBad / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q186B7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: PEG 6000, pH 4.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 38717 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.056.90.707198.5
3.05-3.1170.676199.6
3.11-3.177.20.6231100
3.17-3.237.20.5391100
3.23-3.37.20.5161100
3.3-3.387.20.421100
3.38-3.467.20.3391100
3.46-3.567.20.3041100
3.56-3.667.20.241100
3.66-3.787.20.1921100
3.78-3.917.20.161100
3.91-4.077.10.131100
4.07-4.267.10.1051100
4.26-4.487.10.0951100
4.48-4.767.10.0911100
4.76-5.1370.097199.9
5.13-5.6470.1061100
5.64-6.466.90.097199.9
6.46-8.136.60.057199.9
8.13-506.70.038199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→48.44 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.8 / σ(F): 1.34 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1942 5.02 %
Rwork0.186 --
obs0.189 38654 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.86 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 59.96 Å2
Baniso -1Baniso -2Baniso -3
1--5.7223 Å20 Å2-0 Å2
2--26.4041 Å20 Å2
3----20.6818 Å2
Refinement stepCycle: LAST / Resolution: 2.99→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9457 0 65 36 9558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039738
X-RAY DIFFRACTIONf_angle_d0.84713186
X-RAY DIFFRACTIONf_dihedral_angle_d13.4423479
X-RAY DIFFRACTIONf_chiral_restr0.1611671
X-RAY DIFFRACTIONf_plane_restr0.0021567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9932-3.06810.3621440.27222483X-RAY DIFFRACTION96
3.0681-3.1510.28251300.22772592X-RAY DIFFRACTION100
3.151-3.24370.24461210.21212600X-RAY DIFFRACTION100
3.2437-3.34840.34551490.22182618X-RAY DIFFRACTION100
3.3484-3.4680.30111430.2112606X-RAY DIFFRACTION100
3.468-3.60680.27481300.19282618X-RAY DIFFRACTION100
3.6068-3.77090.26611480.17282591X-RAY DIFFRACTION100
3.7709-3.96970.22211210.16332626X-RAY DIFFRACTION100
3.9697-4.21820.20841270.14782656X-RAY DIFFRACTION100
4.2182-4.54370.15881410.13212612X-RAY DIFFRACTION100
4.5437-5.00050.17961260.13422649X-RAY DIFFRACTION100
5.0005-5.72310.28981640.19562634X-RAY DIFFRACTION100
5.7231-7.20670.21581540.19932662X-RAY DIFFRACTION100
7.2067-48.44850.22471440.22382765X-RAY DIFFRACTION99
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)
10.7969-0.05190.80542.8213-0.39072.4021-0.13460.2236-0.0859-0.0336-0.0618-0.1601-0.3432-0.18340.03770.30580.1695-0.12030.32950.01120.2767-17.592148.3791-40.2958
21.04910.0702-0.25150.81550.12051.09780.1792-0.02270.00480.105-0.02570.0986-0.01040.1103-0.04810.19630.03130.06350.43850.07070.1767-15.60536.8707-18.0009
30.83290.0614-0.62240.24460.23360.78750.08410.04640.0939-0.02910.04120.2321-0.2853-0.5116-0.17290.15680.11310.02290.5725-0.05890.2419-24.756447.0584-27.0337
40.7144-0.6910.23921.38940.8531.7184-0.2466-0.388-0.06460.3125-0.0983-0.04560.2673-0.13360.13380.43540.13160.12650.8486-0.03680.3299-19.76839.8066-3.154
51.0135-0.30950.19580.82830.09840.8668-0.0052-0.069-0.19460.03610.00510.1846-0.1682-0.442-0.09320.24310.1239-0.02060.36970.02280.1626-12.379145.6772-20.3924
60.4417-0.08040.23870.4280.36481.9402-0.18670.0651-0.09320.08090.01480.2021-0.1596-0.561-0.13570.644-0.01540.10470.9588-0.11840.2698-27.995339.7909-1.4561
71.1729-0.3038-0.33311.1970.23550.4968-0.0356-0.20690.21130.1058-0.09050.03330.018-0.0321-0.24550.25960.1917-0.00160.2705-0.16010.2888-22.779753.2503-15.924
81.2573-0.00290.4491.09380.39810.30620.10410.3386-0.0876-0.3267-0.2340.2199-0.2713-0.13480.02340.51780.25880.01320.3854-0.03830.3652-10.196659.2459-35.6089
93.28350.1437-0.4561.8884-0.05872.91030.18990.1699-0.096-0.15140.0829-0.0103-0.2332-0.0121-0.04830.2169-0.1621-0.07930.28260.10660.171810.715654.8421-43.1045
101.5421-0.2252-0.06071.53910.33151.6048-0.1453-0.22580.0759-0.06770.0758-0.11620.00040.020.04120.18510.02880.01080.2415-0.07330.17662.490350.6631-19.7537
110.6689-0.25760.32371.34520.45280.4475-0.0690.00990.072-0.1583-0.02080.2192-0.30690.4757-0.03180.3788-0.1426-0.02840.5704-0.06510.362816.162357.9726-37.7573
120.43190.049-0.03230.90720.11770.17220.0208-0.1710.20310.1745-0.00290.0814-0.22470.037-0.09020.524-0.0492-0.12360.1898-0.22430.29794.212463.6973-25.9337
131.1816-0.3801-0.01191.2848-1.1541.5851-0.1014-0.20880.1380.3599-0.21430.2045-0.41080.2026-0.50510.48410.0189-0.00710.4629-0.21360.2314.97756.9437-5.5419
141.2297-0.0133-0.42240.9948-0.3131.3583-0.0274-0.18170.16690.0015-0.03390.0898-0.22440.05980.080.2194-0.0089-0.00840.38-0.01890.205811.715350.0748-22.7636
150.2220.15550.32630.10830.22850.47960.0974-0.31260.24170.17760.06030.138-0.5943-0.2738-0.00521.10010.30830.15491.105-0.27980.50682.775765.0278-4.3107
161.3685-0.3636-0.21130.8093-0.68620.8077-0.1684-0.26370.15450.2086-0.0504-0.1635-0.2642-0.1030.18550.3295-0.1675-0.10890.3668-0.1040.29915.93562.6543-19.6967
170.929-0.8474-0.9652.540.73151.3306-0.03150.34430.37-0.3127-0.07880.13-0.21930.08320.00310.2166-0.1688-0.02870.54130.07060.383724.506950.6377-39.4208
180.44890.3731-0.13681.74150.59353.6123-0.03080.0628-0.10.02-0.16770.15110.10050.13180.06950.39890.02780.10480.1027-0.01990.04496.41826.1146-42.7252
190.2489-0.12290.04240.1404-0.06190.0301-0.0306-0.1056-0.045-0.0448-0.0471-0.07830.23860.1306-0.18430.35010.5474-0.08410.0960.25790.100214.33069.7456-25.486
200.6204-0.2843-0.49480.6938-0.3151.2668-0.066-0.2882-0.20440.443-0.0344-0.34760.4470.36590.0420.85070.1553-0.17230.78080.27150.513618.73959.8812-6.9626
211.08370.2559-0.1650.0618-0.03990.0266-0.0060.1866-0.2587-0.19550.2802-0.02460.5164-0.1065-0.17910.66130.0273-0.01190.2450.0320.29492.516612.0903-24.4718
222.98811.8009-0.78632.33960.21420.58540.4256-1.0254-0.56820.64520.0498-0.3020.69770.6299-0.24510.81150.4185-0.02910.89670.140.506819.24865.7752-13.5385
230.3789-0.12450.09650.7493-0.14020.1758-0.00810.0061-0.1108-0.1913-0.02980.12440.20280.0341-0.17030.90460.03830.04990.14090.07790.42214.8221-0.4729-24.7119
243.8869-0.61550.96920.7831.49444.20230.72140.4277-0.0126-0.9026-0.29450.1396-0.17330.1826-0.46991.3090.11240.12310.4285-0.11290.5467-10.61140.622-45.3484
253.4419-0.4196-0.30790.5679-0.18362.3114-0.0292-0.05690.1653-0.1652-0.17380.31740.5691-0.45830.15560.4395-0.19510.05470.6377-0.09240.286-21.370117.9729-39.9377
260.7896-0.1593-0.33961.4158-0.13150.1747-0.15860.0052-0.03010.16580.160.06110.562-0.13060.01140.5338-0.03290.03530.31110.16280.3275-8.262715.2069-18.7503
270.51590.0622-0.93181.3543-0.17721.6864-0.18130.2083-0.2940.0932-0.19450.25630.6101-0.65980.17170.5188-0.20890.06430.58940.05370.4304-26.515718.3607-33.597
281.00040.3536-0.19770.9277-0.28630.5228-0.03080.0222-0.18020.0744-0.0965-0.0860.3967-0.0734-0.51710.5735-0.24130.16960.27240.11140.3101-18.31896.0795-23.8329
291.11730.26610.45770.9650.60860.814-0.2675-0.5027-0.31380.15660.0072-0.11390.66330.00520.04470.8666-0.03350.00630.60020.2740.4308-11.422410.865-3.9765
300.9575-0.1430.40261.38910.22980.2379-0.136-0.2397-0.2103-0.04470.33550.17770.3944-0.5361-0.1680.3926-0.07880.06010.45560.08760.3752-21.670723.3242-20.4936
311.5844-0.48911.09092.0613-0.08071.14450.30580.1183-0.0845-0.23670.0043-0.09360.3214-0.2573-0.15480.26820.0408-0.01770.3038-0.08250.2519-9.381427.0962-24.8918
321.2332-0.47120.19660.88310.03820.0508-0.1815-0.3132-0.59980.50880.34430.03990.6607-0.4547-0.2340.7911-0.16180.05070.44650.16080.4465-16.031210.9251-13.2423
330.32260.1137-0.07010.10040.10050.27510.0015-0.1204-0.1192-0.0967-0.2291-0.3780.1928-0.07520.2541.6543-0.0819-0.10431.0710.48410.7862-14.6933.2483-2.6046
341.8885-0.2148-0.47721.00510.1671.1421-0.1710.1402-0.20250.3271-0.12010.120.3679-0.15030.03670.4898-0.24430.11420.57620.09570.3943-26.242314.1025-16.1203
351.2730.3636-0.33130.93330.19370.2331-0.0015-0.12030.00930.0595-0.17240.13550.03860.02820.08120.2053-0.1165-0.01530.59840.07610.295-29.023329.5763-34.8121
360.71490.1084-0.1280.21840.08460.8659-0.07240.0792-0.0337-0.0724-0.0206-0.12770.06870.3883-0.0422-0.01570.15740.01560.4282-0.00160.084623.045134.6541-27.815
370.69720.0720.28590.31-0.19180.275-0.01160.10480.0162-0.0339-0.0519-0.24480.0430.4553-0.1952-0.05850.0943-0.10190.5791-0.07020.219730.042534.6374-32.46
380.41580.14370.05360.3476-0.80622.2764-0.1869-0.20490.17490.2124-0.1724-0.2052-0.07110.67360.1010.34670.1006-0.11690.9159-0.11050.353428.8638.4755-7.9774
390.7567-0.0632-0.07770.96270.01540.16740.01220.19150.09290.09250.0199-0.15510.14390.83740.0130.27050.1756-0.01160.59970.07020.241123.296728.3447-23.9427
401.1748-0.80761.47851.0331-0.52522.3654-0.073-0.0562-0.00180.09410.2436-0.19270.19310.5044-0.19830.4827-0.0348-0.14081.3162-0.11190.425935.982842.0288-6.8626
412.6025-0.1207-1.07431.01740.02750.7394-0.0667-0.6691-0.1980.2063-0.1031-0.10810.08390.3580.17120.12070.17560.0190.62670.09670.371136.746528.4507-21.7279
422.531-1.4068-0.11242.3202-0.16540.3010.0307-0.0624-0.1038-0.03250.08020.22480.04080.05450.29880.53310.4023-0.04360.5388-0.00530.539926.809915.0058-39.6432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:23)
2X-RAY DIFFRACTION2chain 'A' and (resseq 24:82)
3X-RAY DIFFRACTION3chain 'A' and (resseq 83:129)
4X-RAY DIFFRACTION4chain 'A' and (resseq 130:152)
5X-RAY DIFFRACTION5chain 'A' and (resseq 153:214)
6X-RAY DIFFRACTION6chain 'A' and (resseq 215:222)
7X-RAY DIFFRACTION7chain 'A' and (resseq 223:242)
8X-RAY DIFFRACTION8chain 'A' and (resseq 243:256)
9X-RAY DIFFRACTION9chain 'B' and (resseq 0:23)
10X-RAY DIFFRACTION10chain 'B' and (resseq 24:82)
11X-RAY DIFFRACTION11chain 'B' and (resseq 83:100)
12X-RAY DIFFRACTION12chain 'B' and (resseq 101:129)
13X-RAY DIFFRACTION13chain 'B' and (resseq 130:152)
14X-RAY DIFFRACTION14chain 'B' and (resseq 153:214)
15X-RAY DIFFRACTION15chain 'B' and (resseq 215:222)
16X-RAY DIFFRACTION16chain 'B' and (resseq 223:242)
17X-RAY DIFFRACTION17chain 'B' and (resseq 243:256)
18X-RAY DIFFRACTION18chain 'C' and (resseq 0:23)
19X-RAY DIFFRACTION19chain 'C' and (resseq 24:129)
20X-RAY DIFFRACTION20chain 'C' and (resseq 130:152)
21X-RAY DIFFRACTION21chain 'C' and (resseq 153:197)
22X-RAY DIFFRACTION22chain 'C' and (resseq 198:222)
23X-RAY DIFFRACTION23chain 'C' and (resseq 223:253)
24X-RAY DIFFRACTION24chain 'C' and (resseq 254:265)
25X-RAY DIFFRACTION25chain 'D' and (resseq 0:23)
26X-RAY DIFFRACTION26chain 'D' and (resseq 24:82)
27X-RAY DIFFRACTION27chain 'D' and (resseq 83:100)
28X-RAY DIFFRACTION28chain 'D' and (resseq 101:129)
29X-RAY DIFFRACTION29chain 'D' and (resseq 130:152)
30X-RAY DIFFRACTION30chain 'D' and (resseq 153:175)
31X-RAY DIFFRACTION31chain 'D' and (resseq 176:197)
32X-RAY DIFFRACTION32chain 'D' and (resseq 198:214)
33X-RAY DIFFRACTION33chain 'D' and (resseq 215:222)
34X-RAY DIFFRACTION34chain 'D' and (resseq 223:243)
35X-RAY DIFFRACTION35chain 'D' and (resseq 244:256)
36X-RAY DIFFRACTION36chain 'E' and (resseq 0:69)
37X-RAY DIFFRACTION37chain 'E' and (resseq 70:129)
38X-RAY DIFFRACTION38chain 'E' and (resseq 130:152)
39X-RAY DIFFRACTION39chain 'E' and (resseq 153:214)
40X-RAY DIFFRACTION40chain 'E' and (resseq 215:222)
41X-RAY DIFFRACTION41chain 'E' and (resseq 223:242)
42X-RAY DIFFRACTION42chain 'E' and (resseq 243:256)

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