[English] 日本語
Yorodumi
- PDB-2qie: Staphylococcus aureus molybdopterin synthase in complex with prec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qie
TitleStaphylococcus aureus molybdopterin synthase in complex with precursor Z
Components
  • Molybdopterin synthase small subunit
  • Molybdopterin-converting factor subunit 2
KeywordsTRANSFERASE / MOLYBDOPTERIN / MOCO / MPT SYNTHASE / MOAD / MOAE / MOLYBDENUM COFACTOR BIOSYNTHESIS / beta-Grasp (ubiquitin-like) / alpha beta hammerhead fold
Function / homology
Function and homology information


molybdopterin synthase / molybdopterin synthase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
Molybdopterin synthase sulfur carrier subunit / Molybdopterin biosynthesis MoaE subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Aldehyde Oxidoreductase; domain 3 / Beta-grasp domain ...Molybdopterin synthase sulfur carrier subunit / Molybdopterin biosynthesis MoaE subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Aldehyde Oxidoreductase; domain 3 / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-8CS / Molybdopterin synthase catalytic subunit / Molybdopterin synthase sulfur carrier subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDaniels, J.N. / Schindelin, H.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure of a molybdopterin synthase-precursor Z complex: insight into its sulfur transfer mechanism and its role in molybdenum cofactor deficiency.
Authors: Daniels, J.N. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H.
History
DepositionJul 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Molybdopterin-converting factor subunit 2
B: Molybdopterin synthase small subunit
H: Molybdopterin-converting factor subunit 2
G: Molybdopterin synthase small subunit
K: Molybdopterin-converting factor subunit 2
J: Molybdopterin synthase small subunit
E: Molybdopterin-converting factor subunit 2
D: Molybdopterin synthase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,39212
Polymers105,0118
Non-polymers1,3814
Water1,40578
1
A: Molybdopterin-converting factor subunit 2
B: Molybdopterin synthase small subunit
E: Molybdopterin-converting factor subunit 2
D: Molybdopterin synthase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1966
Polymers52,5054
Non-polymers6902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
MethodPISA
2
H: Molybdopterin-converting factor subunit 2
G: Molybdopterin synthase small subunit
K: Molybdopterin-converting factor subunit 2
J: Molybdopterin synthase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1966
Polymers52,5054
Non-polymers6902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.639, 58.100, 331.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

-
Components

#1: Protein
Molybdopterin-converting factor subunit 2 / MPT synthase subunit 2 / Molybdopterin synthase subunit 2 / Molybdenum cofactor biosynthesis ...MPT synthase subunit 2 / Molybdopterin synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin-converting factor large subunit


Mass: 17374.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: moaE / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P65401
#2: Protein
Molybdopterin synthase small subunit


Mass: 8878.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: moaD / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7A441
#3: Chemical
ChemComp-8CS / (2R,4AR,5AR,11AR,12AS)-8-AMINO-2-HYDROXY-4A,5A,9,11,11A,12A-HEXAHYDRO[1,3,2]DIOXAPHOSPHININO[4',5':5,6]PYRANO[3,2-G]PTERIDINE-10,12(4H,6H)-DIONE 2-OXIDE


Mass: 345.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 8000, 0.1% polyvinylpyrrollidone K15, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2005
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38004 / % possible obs: 96.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.071 / Χ2: 2.354 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.563.60.63121321.78583.1
2.56-2.624.40.55522501.75187.1
2.62-2.694.70.50423051.7989.9
2.69-2.774.90.42124571.8495.9
2.77-2.865.20.34824891.92797.5
2.86-2.965.40.27725651.9699.7
2.96-3.085.60.2125772.1100
3.08-3.225.70.15326012.132100
3.22-3.395.70.10726052.271100
3.39-3.615.70.08125782.51100
3.61-3.885.80.06626262.599100
3.88-4.275.70.05626272.782100
4.27-4.895.60.05226483.099100
4.89-6.165.50.05426883.12299.9
6.16-505.20.0428562.74299.3

-
Phasing

Phasing MRRfactor: 0.463 / Cor.coef. Fo:Fc: 0.514
Highest resolutionLowest resolution
Rotation4 Å40.32 Å
Translation4 Å40.32 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q5W
Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.209 / SU B: 16.779 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.522 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1900 5 %RANDOM
Rwork0.207 ---
obs0.209 37933 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.947 Å2
Baniso -1Baniso -2Baniso -3
1-3.92 Å20 Å20 Å2
2--0.48 Å20 Å2
3----4.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.291 Å0.522 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6997 0 92 78 7167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227246
X-RAY DIFFRACTIONr_bond_other_d0.0010.026517
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.9659839
X-RAY DIFFRACTIONr_angle_other_deg0.708315247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4465839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90325.432359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.448151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9621528
X-RAY DIFFRACTIONr_chiral_restr0.0650.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021395
X-RAY DIFFRACTIONr_nbd_refined0.1850.21263
X-RAY DIFFRACTIONr_nbd_other0.1650.26490
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23434
X-RAY DIFFRACTIONr_nbtor_other0.0780.24219
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2151
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.040.23
X-RAY DIFFRACTIONr_mcbond_it0.271.55573
X-RAY DIFFRACTIONr_mcbond_other0.0481.51714
X-RAY DIFFRACTIONr_mcangle_it0.33426918
X-RAY DIFFRACTIONr_scbond_it0.633609
X-RAY DIFFRACTIONr_scangle_it0.9614.52921
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5640.4111240.3382184282781.641
2.564-2.6330.3591280.2992301277787.468
2.633-2.7090.331250.2962321268890.997
2.709-2.7920.3531300.2922369259396.375
2.792-2.8820.4331020.2722397254598.193
2.882-2.9830.3051180.2612328245299.755
2.983-3.0940.2831140.24122502364100
3.094-3.2190.31010.2222187228999.956
3.219-3.360.2681200.22120792199100
3.36-3.5220.233960.21520402136100
3.522-3.710.241020.20818861988100
3.71-3.9310.2751040.21118071911100
3.931-4.1970.224950.18317211816100
4.197-4.5260.187960.15916021698100
4.526-4.9470.205800.14514911571100
4.947-5.5120.222680.1531356142799.79
5.512-6.3290.236710.18212371308100
6.329-7.6670.235540.17110451099100
7.667-10.5050.216420.195860902100
10.505-300.29300.27857260899.013
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)
117.24220.28841.73392.3804-2.35082.55850.06491.2779-0.1324-0.764-0.0792-0.09730.460.32850.01430.12190.1726-0.0216-0.225-0.044-0.104720.5533.80112.941
21.05270.0384-0.68843.4559-0.99930.9979-0.66970.0519-0.1244-0.62250.29010.0689-0.0550.07690.3797-0.04460.1112-0.0189-0.34270.0442-0.162313.1940.7117.314
313.1707-3.8796-1.014221.9022-1.83582.64730.0398-0.47071.38750.7525-0.316-0.3388-0.0880.64470.27620.13620.0551-0.1063-0.04890.0580.137738.28448.53524.441
411.2853-0.2118-0.80544.7635-2.32237.6793-0.00190.2704-0.8851-0.21480.0006-0.14840.64150.03850.0014-0.06080.2317-0.0485-0.245-0.0311-0.059628.94826.63624.947
530.9602-14.3477-3.627110.87626.00064.83910.1516-0.2295-0.82690.1488-0.01450.71550.3648-0.4644-0.13720.01480.1514-0.0022-0.26720.0858-0.035613.83729.32327.67
63.5695-0.54212.09641.4835-0.09391.29230.3463-0.3494-0.47060.0814-0.1064-0.0632-0.1220.1608-0.2399-0.05850.16420.035-0.22450.0106-0.157819.76234.68621.618
77.19241.5958-0.01272.5997-0.66252.5830.0491-0.30080.3478-0.0134-0.00130.2015-0.2326-0.1042-0.0478-0.02660.139-0.0598-0.28030.0089-0.142516.01341.65722.466
812.10810.74612.46423.0741-0.73180.7594-0.2093-0.08920.44540.02410.164-0.072-0.45460.33920.0453-0.00340.2349-0.0723-0.1350.067-0.056527.31234.65829.961
921.580211.1721-11.808821.6954-15.347716.63750.9618-1.21151.32691.2056-0.8071-0.6422-1.80220.5814-0.15470.07070.0344-0.07820.171-0.0210.103741.47641.79529.723
1017.06052.64240.389922.9478-2.3856.66690.0510.2017-0.34710.0493-0.2684-0.14010.18090.09830.2174-0.16080.18110.1155-0.03470.1033-0.272639.00821.74330.975
117.63613.48592.148813.91372.39625.4255-0.0250.3374-0.5531-0.1236-0.3696-1.12580.40951.41680.3947-0.22460.33860.14170.14530.0946-0.056844.01820.06431.412
1215.42960.0742-4.743710.05467.10489.0075-0.14570.4923-0.4531-0.13630.0927-0.08771.58450.9270.053-0.06790.31890.0879-0.06680.1334-0.156635.51111.3342.803
1311.62188.8022-5.255331.18023.94156.89410.63410.54720.2522-0.3446-0.45431.01360.23560.0834-0.1798-0.12680.33090.10950.10620.1856-0.033841.00118.80243.333
1411.1111-3.68777.62015.6152-9.251319.4587-0.2261-0.8386-1.01630.3761-0.50551.0826-0.12711.30720.7316-0.35520.14770.06230.32170.07070.130446.83221.77541.212
1514.789714.70014.453625.57433.379910.9628-0.036-0.84751.08880.3955-0.80870.8815-0.52650.130.8448-0.13910.25850.0814-0.0730.0528-0.189134.41424.76738.559
160.1269-0.3511-0.446910.4232-17.263937.7882-0.486-0.2430.0191-0.20090.05881.35721.2425-0.95620.4272-0.3240.24240.0362-0.07740.04570.225325.83920.69435.992
176.0517-1.9027-4.658432.364212.359225.0073-0.5706-0.1978-0.35150.3550.20170.88591.48850.03970.3689-0.17720.18160.0235-0.27390.10970.006629.8712.54741.083
184.0763-0.5861-0.246330.7831-6.81335.2364-0.1381-0.0254-0.0841-0.85040.39840.6923-0.03740.3991-0.2602-0.12750.19010.0719-0.13990.0414-0.207832.81624.1832.413
1916.01784.79371.354331.5489-2.47988.8455-0.2445-0.07660.85930.24360.51040.1306-0.4287-0.4095-0.2659-0.22060.07990.0213-0.2790.0455-0.1335-6.59870.576.697
2015.793614.231512.364313.639.549112.82430.58330.1589-0.0727-0.4098-0.80471.09910.7826-0.60270.2214-0.07230.03230.0621-0.31190.08120.3443-12.98361.8827.432
210.0432-0.04670.46434.44432.75187.4057-0.06610.22170.3113-0.64390.06110.9122-0.6453-0.02680.005-0.19870.12220.0403-0.23450.0540.1684-10.67678.0998.949
2229.480818.944531.58612.41718.319249.9369-0.4771-0.8974-0.70820.46510.47891.2867-0.4139-1.1415-0.0019-0.29640.13580.09850.03620.11330.2597-17.01575.44313.01
239.5852.12252.14248.83620.24762.85310.0668-0.6336-0.74910.64160.15630.86660.0552-0.7737-0.2231-0.0510.03510.1293-0.17030.10320.0338-12.65569.00514.073
242.609-8.0114-0.534725.28045.054617.2364-0.8179-1.39581.21660.98081.3577-1.2511.54980.9501-0.5398-0.22860.1697-0.1193-0.1835-0.04710.06090.63972.77718.234
2510.58269.9983-4.961521.472-12.916829.9559-0.1993-0.75880.31080.0554-0.0011-0.39530.39920.74230.2004-0.22510.21480.0101-0.3336-0.00880.0329-4.53881.88616.116
261.70524.13311.378632.2933-8.46917.3771-0.27020.03670.2494-0.38520.8490.30140.7106-0.0526-0.5789-0.18760.08230.0976-0.3277-0.0043-0.141-3.84566.10613.359
2724.885112.7978-19.125320.51281.069823.2356-0.26871.42951.1948-0.97441.0072-1.3721.0231.1217-0.73850.17750.1082-0.1891-0.3050.00240.090315.9759.949.012
2819.6726-3.14336.90065.97440.90363.1560.77871.1235-0.7569-0.0996-0.4626-0.34520.36020.8918-0.31610.0940.11460.0104-0.24740.064-0.063416.91551.5077.781
290.7124-1.70420.17724.3076-0.79120.6288-0.0387-0.01520.2648-0.22-0.0734-0.5313-0.04630.21070.1120.07610.1508-0.1017-0.29260.0332-0.154119.45249.39317.738
307.95686.86781.290515.99552.65071.8924-0.17980.0406-0.47070.24990.1319-0.18760.5898-0.19410.0480.11920.06460.15-0.29960.0707-0.1084-1.7651.62510.259
3123.0443-2.52828.42194.396-6.905911.7661-0.7583-0.39451.87980.9625-0.389-0.4473-1.06610.41961.14720.12850.1067-0.1429-0.3042-0.02710.07614.13863.3821.5
323.89360.09292.55931.52430.88712.63130.1120.04210.38310.1531-0.2416-0.04640.47360.2450.12970.11270.0961-0.041-0.33640.006-0.125710.8354.12214.023
335.7410.2971.96943.2321.41444.0422-0.1025-0.51090.00850.18390.2026-0.2486-0.03010.0854-0.10.02660.1202-0.0692-0.30370.0266-0.165915.03750.61921.695
3413.28336.0188.5956.78987.568110.6807-0.1745-0.9786-0.56140.3185-0.0420.23990.744-1.10220.21650.09970.11570.0571-0.23080.0898-0.0142-3.50353.7113.702
3532.0459.854218.160124.246916.654535.22670.4874-1.1418-1.34780.88720.5281-0.98351.3052-0.3802-1.01550.04550.00990.1851-0.18280.05270.1894-8.89553.71513.924
363.6584-2.078-1.193613.18533.11993.1982-0.2455-0.7889-0.29031.41010.4581-0.07220.57920.0726-0.2126-0.04630.19720.09650.23020.1731-0.0289-1.78210.61771.164
372.51531.59230.605313.12654.8834.62320.0745-0.2792-0.4477-0.2671-0.04630.61820.1674-0.1711-0.0282-0.2450.24390.1078-0.06740.19260.0214-11.1438.53360.808
3830.292215.758413.80518.8668.74789.96242.1671-0.7625-3.94021.0999-0.3495-0.27461.0621-0.3407-1.81760.34120.3062-0.12020.08750.17430.6775-10.362-9.29455.405
390.78071.2508-0.525812.91391.736.48760.2416-0.2026-0.2074-0.4162-0.1726-0.86370.5073-0.1309-0.069-0.13140.26930.07710.04750.10260.12747.6545.46959.453
4029.2033-11.4018-4.2894.46711.76661.1774-0.0942-0.943-0.09660.78590.8296-0.2876-1.8330.6302-0.7354-0.04350.1430.32660.18480.04340.17725.14721.25557.81
412.9491-2.67380.63243.0511-1.16162.21290.0627-0.4031-0.09190.09350.0239-0.41180.12020.2469-0.0866-0.21050.24560.1231-0.00630.1566-0.0051-0.73611.06462.36
423.19782.42930.05867.87563.02313.2892-0.0971-0.4712-0.3731-0.47150.5380.3030.0428-0.05-0.4408-0.20850.21680.15670.03350.2112-0.0212-7.519.88663.917
433.2569-1.5768-0.39566.44421.37183.62790.34040.1063-0.6396-1.4276-0.18870.14750.34190.0405-0.1517-0.00320.20660.1249-0.02390.13030.147-2.6797.51653.637
4454.7813-41.7337-11.935533.7661.042135.46152.06041.4048-2.3454-1.1745-0.4827-0.54451.9174-0.9825-1.57770.61050.050.0331-0.24670.07650.266916.508-6.42554.972
4536.6056-1.806420.56930.3818-2.99324.9286-2.0680.60970.5861-0.1201-0.0640.3682.3303-0.64572.1321.34-0.37680.28510.14610.07380.511312.249-12.68952.887
4610.29351.99131.24171.14591.86683.628-0.66930.1488-1.21750.0578-0.49780.19321.98890.01041.16720.50360.28170.2952-0.05750.15180.697527.249-4.04147.741
4721.25457.802827.669543.9451-10.406546.3147-2.17312.5817-0.8231-0.33020.361-1.70792.8436-1.26611.81210.54420.22510.59150.3361-0.12540.340820.51-7.40141.99
4821.21942.84323.992110.00074.677834.2002-0.5679-0.46070.71221.5340.2017-2.2461.1802-2.25850.36610.8721-0.1522-0.03060.121-0.08840.510416.841-13.14942.681
495.5304-3.76495.67114.32324.93349.74870.09122.1971-0.0156-1.5287-0.0019-0.712-0.4465-1.674-0.08940.01720.10660.28460.36130.09620.21112.525-1.51146.016
5021.3675-16.923327.58517.4198-11.358563.0053-0.09650.20710.2391-0.64660.9576-1.7490.35730.4017-0.8611-0.01280.07430.23140.0202-0.00990.355116.9496.48251.701
516.47546.488-3.86497.0608-2.49315.7032-0.16420.13090.999-0.76930.2511-0.1787-0.0337-0.4259-0.08690.13910.2650.21780.06660.05050.384717.6661.00350.539
5217.076215.27691.506847.5467-2.755535.44920.1013-1.6776-1.14942.5936-0.1231-0.35750.4772-0.17520.0219-0.16130.19810.1676-0.00140.14680.091-27.97512.92670.197
532.5803-1.9318-0.473911.67385.16846.0689-0.2354-1.0799-0.6360.6860.52360.27730.39280.138-0.2882-0.08780.14190.14860.19460.27430.0537-20.02810.33871.59
542.66021.65360.52512.05465.37324.99180.2102-0.47860.26380.10080.0741-0.4395-0.20060.3156-0.2843-0.25180.19220.23660.13730.1-0.1074-12.55725.36769.796
553.7172-2.5578-3.48191.88033.334910.591-0.2365-0.2552-0.2690.141-0.40860.5816-0.0403-0.22060.6452-0.10570.22090.250.01170.1415-0.0265-30.61821.51865.519
561.1711-0.6597-1.66720.9291.01512.3840.1916-0.3694-0.1207-0.128-0.24970.0646-0.1339-0.36690.0582-0.15640.2080.17660.04860.1764-0.1011-23.2817.29264.444
572.16641.08010.76983.4772.63855.01850.1249-0.146-0.0791-0.13650.1631-0.15150.2210.2797-0.288-0.22880.27250.207-0.02810.1364-0.0885-15.83716.34361.462
581.5955-4.5641-4.122813.205812.663915.70370.371-0.31770.0576-0.458-0.0276-0.0672-0.50570.6937-0.3434-0.17140.25280.24240.04190.1268-0.0534-24.86727.58363.768
599.67847.23746.51849.34272.893914.0234-0.41260.29820.496-0.4472-0.0374-0.3522-0.59561.25040.450.00530.1690.43520.35220.05890.169-18.38939.774.021
6036.528811.0007-4.890818.55168.762916.28220.3828-1.12541.04110.0725-0.10880.42950.68910.1089-0.274-0.04820.23690.24270.14140.0516-0.0979-38.17935.22774.198
6124.405213.443-1.04969.63120.4211.39220.7387-1.41012.04260.1226-0.9320.485-0.2117-0.5010.1933-0.07510.14750.32740.2548-0.18130.1792-39.96138.877.677
6243.91048.0057-6.056717.9393-2.31891.26151.55440.40522.2854-0.0171-0.69380.0505-0.5809-0.1703-0.8606-0.04210.23950.34610.21590.22660.2237-51.62738.84464.485
6329.760410.698-3.843626.995814.412954.14920.568-0.03012.43570.8574-1.108-1.0743-0.48641.36580.53990.08170.18830.38630.09230.22141.0036-44.30943.49766.926
6411.69892.69810.20414.67064.98027.97290.47090.19632.5619-0.7644-0.1450.3212-0.81450.0937-0.3258-0.0840.16530.40730.11850.10460.4478-38.75342.40768.507
6537.71593.608812.312171.27-58.684465.53830.66551.9239-0.889-0.76271.36331.4414-1.5017-1.0256-2.02870.18640.35740.41160.154-0.04450.0629-40.25428.62861.639
6624.798119.9054-24.440836.7764-33.494952.0841-0.0741.1941.0059-2.32290.47020.94462.523-0.5044-0.3962-0.05960.2230.18220.12660.06940.1522-50.02632.87463.367
6743.54312.6067-9.69042.1102-0.39256.06290.55850.64240.0189-0.385-0.16670.1592-0.1264-0.1966-0.3917-0.08910.19290.24220.03680.0367-0.1346-34.23932.59568.072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 211 - 21
2X-RAY DIFFRACTION2AA22 - 3522 - 35
3X-RAY DIFFRACTION3AA36 - 4836 - 48
4X-RAY DIFFRACTION4AA49 - 5949 - 59
5X-RAY DIFFRACTION5AA60 - 6960 - 69
6X-RAY DIFFRACTION6AA70 - 8570 - 85
7X-RAY DIFFRACTION7AA86 - 11186 - 111
8X-RAY DIFFRACTION8AA112 - 124112 - 124
9X-RAY DIFFRACTION9AA125 - 136125 - 136
10X-RAY DIFFRACTION10BB1 - 81 - 8
11X-RAY DIFFRACTION11BB9 - 229 - 22
12X-RAY DIFFRACTION12BB23 - 3123 - 31
13X-RAY DIFFRACTION13BB32 - 3632 - 36
14X-RAY DIFFRACTION14BB37 - 4337 - 43
15X-RAY DIFFRACTION15BB44 - 5244 - 52
16X-RAY DIFFRACTION16BB53 - 5753 - 57
17X-RAY DIFFRACTION17BB58 - 6458 - 64
18X-RAY DIFFRACTION18BB65 - 7765 - 77
19X-RAY DIFFRACTION19DH1 - 71 - 7
20X-RAY DIFFRACTION20DH8 - 128 - 12
21X-RAY DIFFRACTION21DH13 - 2313 - 23
22X-RAY DIFFRACTION21DH24 - 3124 - 31
23X-RAY DIFFRACTION22DH32 - 3832 - 38
24X-RAY DIFFRACTION23DH39 - 5239 - 52
25X-RAY DIFFRACTION24DH53 - 5753 - 57
26X-RAY DIFFRACTION25DH58 - 6558 - 65
27X-RAY DIFFRACTION26DH66 - 7766 - 77
28X-RAY DIFFRACTION27EG1 - 51 - 5
29X-RAY DIFFRACTION28EG6 - 216 - 21
30X-RAY DIFFRACTION29EG22 - 3522 - 35
31X-RAY DIFFRACTION30EG36 - 5936 - 59
32X-RAY DIFFRACTION31EG60 - 6960 - 69
33X-RAY DIFFRACTION32EG70 - 8770 - 87
34X-RAY DIFFRACTION33EG88 - 11288 - 112
35X-RAY DIFFRACTION34EG113 - 130113 - 130
36X-RAY DIFFRACTION35EG131 - 136131 - 136
37X-RAY DIFFRACTION36HC1 - 231 - 23
38X-RAY DIFFRACTION37HC24 - 4024 - 40
39X-RAY DIFFRACTION38HC41 - 4841 - 48
40X-RAY DIFFRACTION39HC49 - 6449 - 64
41X-RAY DIFFRACTION40HC65 - 6965 - 69
42X-RAY DIFFRACTION41HC70 - 8570 - 85
43X-RAY DIFFRACTION42HC86 - 10086 - 100
44X-RAY DIFFRACTION43HC101 - 136101 - 136
45X-RAY DIFFRACTION44GD1 - 71 - 7
46X-RAY DIFFRACTION45GD8 - 188 - 18
47X-RAY DIFFRACTION46GD19 - 3119 - 31
48X-RAY DIFFRACTION47GD32 - 3632 - 36
49X-RAY DIFFRACTION48GD37 - 4437 - 44
50X-RAY DIFFRACTION49GD45 - 5145 - 51
51X-RAY DIFFRACTION50GD52 - 5752 - 57
52X-RAY DIFFRACTION51GD58 - 7758 - 77
53X-RAY DIFFRACTION52KE1 - 51 - 5
54X-RAY DIFFRACTION53KE6 - 236 - 23
55X-RAY DIFFRACTION54KE24 - 4824 - 48
56X-RAY DIFFRACTION55KE49 - 6849 - 68
57X-RAY DIFFRACTION56KE69 - 8569 - 85
58X-RAY DIFFRACTION57KE86 - 11086 - 110
59X-RAY DIFFRACTION58KE111 - 123111 - 123
60X-RAY DIFFRACTION59KE124 - 136124 - 136
61X-RAY DIFFRACTION60JF1 - 81 - 8
62X-RAY DIFFRACTION61JF9 - 229 - 22
63X-RAY DIFFRACTION62JF23 - 3023 - 30
64X-RAY DIFFRACTION63JF31 - 3631 - 36
65X-RAY DIFFRACTION64JF37 - 5237 - 52
66X-RAY DIFFRACTION65JF53 - 5753 - 57
67X-RAY DIFFRACTION66JF58 - 6558 - 65
68X-RAY DIFFRACTION67JF66 - 7766 - 77

+
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