[English] 日本語
Yorodumi
- PDB-3hjb: 1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hjb
Title1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase from Vibrio cholerae.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / glucose-6-phosphate isomerase / pgi / idp01329 / Gluconeogenesis / Glycolysis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase from Vibrio cholerae.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,75048
Polymers253,5694
Non-polymers2,18144
Water73,3394071
1
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,84425
Polymers126,7842
Non-polymers1,06023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-235 kcal/mol
Surface area35830 Å2
MethodPISA
2
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,90623
Polymers126,7842
Non-polymers1,12121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-218 kcal/mol
Surface area35980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.661, 75.094, 127.456
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 63392.148 Da / Num. of mol.: 4 / Mutation: M179V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar El Tor str. N16961 / Gene: pgi, VC_0374 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9KUY4, glucose-6-phosphate isomerase

-
Non-polymers , 6 types, 4115 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4071 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein solution: 7.7 mg/mL protein, 0.01M Tris-HCl, 0.25M Sodium Cloride, Screen solution (PACT II, drop B11): 0.2M Calcium chloride, 0.1M MES pH 6.0, 25% w/v PEG 6000., VAPOR DIFFUSION, ...Details: Protein solution: 7.7 mg/mL protein, 0.01M Tris-HCl, 0.25M Sodium Cloride, Screen solution (PACT II, drop B11): 0.2M Calcium chloride, 0.1M MES pH 6.0, 25% w/v PEG 6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 370201 / Num. obs: 370201 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.4 / Num. unique all: 16052 / % possible all: 85

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZD
Resolution: 1.5→29.88 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.905 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1507 18596 5 %RANDOM
Rwork0.12653 ---
all0.12774 351339 --
obs0.12774 351339 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0.04 Å2
2--0.28 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17164 0 92 4071 21327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218786
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212238
X-RAY DIFFRACTIONr_angle_refined_deg1.371.92725663
X-RAY DIFFRACTIONr_angle_other_deg0.909330059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.76152443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60525.276906
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.827153063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7011557
X-RAY DIFFRACTIONr_chiral_restr0.1020.22781
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023851
X-RAY DIFFRACTIONr_mcbond_it0.9541.511654
X-RAY DIFFRACTIONr_mcbond_other0.3211.54725
X-RAY DIFFRACTIONr_mcangle_it1.62218856
X-RAY DIFFRACTIONr_scbond_it2.62337132
X-RAY DIFFRACTIONr_scangle_it4.2774.56794
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 1306 -
Rwork0.184 23057 -
obs-23057 87.44 %
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)
10.4750.248-0.18220.5824-0.13860.7499-0.03770.0298-0.0629-0.05160.0166-0.06660.0960.07020.02110.0320.02360.00210.0276-0.00580.044651.0965-32.9736.03
20.3867-0.0901-0.01990.57660.08430.59830.0094-0.05250.07140.06680.001-0.0323-0.10460.0656-0.01050.0472-0.0185-0.00420.0207-0.01080.017849.9832-4.820256.3448
31.4958-0.4782.29880.4413-1.5847.41970.03590.0123-0.0840.0740.05870.10250.0432-0.3269-0.09460.1138-0.01630.0270.0498-0.01010.102935.3132-2.897854.7387
40.98040.14720.70450.61540.14081.5445-0.0242-0.00410.16720.0216-0.00370.0361-0.1597-0.0520.02790.07850.01130.00840.0067-0.00630.061636.32877.768749.4766
51.3357-0.9978-0.37541.88430.35160.55280.02930.02640.2581-0.03830.0211-0.2339-0.13460.0891-0.05040.0966-0.02910.00210.0317-0.01090.092850.46458.409850.5372
60.3250.0577-0.03360.2788-0.0050.40270.0106-0.0045-0.01050.01120.0064-0.00590.01820.0071-0.0170.00820.0038-0.00230.002-0.00070.001440.3599-23.964844.285
710.41890.89-1.64333.39410.04022.89110.2177-0.3424-0.63450.1603-0.1644-0.08220.1906-0.1646-0.05330.1035-0.0625-0.0380.04910.0310.089913.816-49.770542.3251
80.48330.0915-0.01380.2631-0.04960.3160.00460.0079-0.0287-0.00240.01040.02420.0459-0.012-0.01490.01250.0007-0.0010.00170.00120.006638.1665-27.926440.633
93.8177-4.8345-0.6038.27211.4231.92810.01550.02940.4681-0.09740.0827-0.4853-0.22890.1235-0.09820.0476-0.00720.02070.01630.01420.079137.76644.928225.9851
101.65530.4644-0.14441.86090.09372.16750.07670.07150.2405-0.0221-0.00740.0027-0.3502-0.1371-0.06930.09030.04290.02440.02930.02850.057923.64237.246723.1585
110.35220.0226-0.28150.49890.01470.5232-0.01450.0979-0.0208-0.07730.01730.01860.0259-0.1154-0.00280.02870.004-0.0160.08290.00690.023214.9018-18.821720.103
121.36980.19040.48681.20290.75292.4118-0.0002-0.0493-0.06480.0539-0.05730.14310.0826-0.28290.05750.01530.01430.01370.08190.01380.0567-3.4222-14.110847.9464
130.5647-0.0987-0.16090.4643-0.20841.31420.0227-0.0570.06030.0810.0058-0.0051-0.1272-0.0407-0.02850.02760.01180.00640.0316-0.00340.014913.8032-8.518757.514
142.8872-2.9014-1.42535.69033.23212.24180.1410.056-0.0115-0.1205-0.0138-0.1793-0.1617-0.0134-0.12720.05540.00510.00820.05350.01240.052219.5126-13.881956.2289
152.279-1.5371-0.3641.412-0.02180.6424-0.0005-0.0879-0.07450.01970.0460.0530.0157-0.0169-0.04540.02480.0019-0.00110.02990.00950.010617.8799-20.592363.138
160.5854-0.13720.8710.24960.16783.85210.0599-0.1526-0.12740.0639-0.00360.04560.2373-0.2724-0.05630.0545-0.01120.0090.09420.02810.05655.6068-22.094363.8025
170.2419-0.0605-0.19190.23640.13030.38810.01870.05490.0229-0.01320.00640.0143-0.0231-0.088-0.02510.00480.0090.00150.03360.01090.00514.3771-14.074835.0053
180.55060.1561-0.0810.224-0.06340.31880.00130.05610.02070.00330.0119-0.0342-0.0313-0.0158-0.01320.00970.00710.00190.01180.0040.01129.5916-11.437728.2708
191.6089-0.14623.19551.259-0.736410.1740.0057-0.2198-0.062-0.0010.02550.07390.3021-0.5404-0.03120.0246-0.01040.00570.03440.00890.017523.4025-39.962952.7282
201.5279-0.0353-0.34931.81640.28152.8961-0.0251-0.1081-0.0830.14450.003-0.03810.2405-0.03430.02210.07120.0091-0.00240.01280.00770.01437.0211-41.712458.7711
211.5368-0.481.24391.3086-0.56931.7028-0.1116-0.12340.10670.12090.0368-0.0138-0.1768-0.17860.07480.06170.0240.01770.0837-0.01510.023579.55525.190648.6474
220.4872-0.15530.32660.6435-0.01070.48770.0019-0.09620.00470.06470.01460.01960.0164-0.1206-0.01650.0241-0.01250.01670.07830.01190.022577.565810.66542.6827
231.10880.0201-0.20621.07340.60282.1374-0.0080.03810.0457-0.0388-0.06340.1438-0.058-0.26330.07140.0109-0.0118-0.01140.07560.01390.044860.23679.856616.2406
240.57010.05390.17820.5042-0.28161.30560.02330.0494-0.063-0.07280.0011-0.0050.1246-0.0115-0.02450.0237-0.0125-0.00330.0313-0.00480.017377.07864.10256.4067
251.68451.15210.53240.8020.46381.0650.0146-0.0029-0.11140.0083-0.0078-0.06690.0515-0.0057-0.00680.03270.0068-0.00850.0212-0.00020.034487.456113.46644.9118
262.31611.36640.05662.23830.01081.27380.01060.08440.1559-0.03590.03210.0524-0.07060.0106-0.04270.0174-0.0044-0.00110.03920.01330.016879.318216.51790.1528
271.16540.2609-1.01280.69420.16424.16490.05020.16880.1687-0.06760.02630.0892-0.2302-0.284-0.07650.02950.0078-0.00910.07610.02840.035169.242417.1943-1.7634
280.3220.08790.21150.23150.12460.42290.0071-0.0504-0.00940.00880.00750.01880.0158-0.0815-0.01460.0037-0.0072-0.00050.03170.00930.004677.20310.040228.2792
290.5148-0.12470.08820.2007-0.06570.34570.0039-0.0481-0.0214-0.00010.0106-0.03350.0316-0.0145-0.01450.014-0.0086-0.00050.01290.00270.01292.27467.268334.9904
300.99250.119-0.07161.119-0.1311.5954-0.01960.09620.0822-0.08850.02770.0353-0.1554-0.0973-0.00810.07180.0019-0.00080.01540.01050.020595.437536.76366.9523
310.7918-0.51570.4320.8265-0.32041.0818-0.0705-0.0650.06830.09340.0512-0.0369-0.186-0.00140.01930.0776-0.0322-0.00060.0337-0.01650.0762110.405434.455430.5957
320.3379-0.17120.02380.37910.1030.5547-0.00430.02120.00160.00980.0163-0.08190.04510.1343-0.0120.01450.00090.00420.0454-0.00050.0375120.383714.684519.5772
330.4745-0.0667-0.21071.17550.01180.76320.00710.0716-0.0779-0.1575-0.01210.04680.1115-0.00470.0050.05070.0018-0.01060.0165-0.01570.0173103.9529-2.30543.8542
341.0464-0.015-0.82050.7288-0.00271.5709-0.0105-0.0066-0.13-0.0256-0.00530.02010.1082-0.05110.01580.0616-0.0082-0.0060.0081-0.00410.046699.4498-9.978914.3834
351.45031.05150.39912.18440.60431.0340.0426-0.0115-0.27260.03640.0028-0.18830.2160.0752-0.04550.09860.02490.00030.0124-0.00580.0778111.0481-14.648712.2858
360.3107-0.06970.02940.2489-0.00510.36040.01340.00940.0082-0.01720.0075-0.0104-0.0150.0143-0.02090.0073-0.00310.00330.0022-0.00150.0022103.95819.178519.3628
3710.0983-3.19140.52462.90010.01672.61660.29090.46120.5182-0.1999-0.2129-0.0853-0.1761-0.1328-0.0780.08060.04810.0360.040.03410.071277.49744.915221.3374
380.4634-0.12340.01060.3272-0.05170.31960.00270.00150.03090.00050.00920.0242-0.0516-0.008-0.01190.0114-0.00020.00260.00110.00080.0062101.267323.933922.6332
394.53226.04320.89159.99611.00311.3724-0.0056-0.0267-0.49710.07680.0922-0.59590.20610.114-0.08660.05360.0235-0.00490.02680.0160.0698100.9079-8.620237.3452
402.7843-0.21710.65032.7610.41652.67630.082-0.0241-0.33290.02110.0269-0.02180.36-0.0714-0.10890.0941-0.0402-0.02210.0330.0220.059186.6277-11.99940.5582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 97
2X-RAY DIFFRACTION2A98 - 177
3X-RAY DIFFRACTION3A178 - 182
4X-RAY DIFFRACTION4A183 - 234
5X-RAY DIFFRACTION5A235 - 266
6X-RAY DIFFRACTION6A267 - 436
7X-RAY DIFFRACTION7A437 - 450
8X-RAY DIFFRACTION8A451 - 511
9X-RAY DIFFRACTION9A512 - 524
10X-RAY DIFFRACTION10A525 - 550
11X-RAY DIFFRACTION11B0 - 103
12X-RAY DIFFRACTION12B104 - 137
13X-RAY DIFFRACTION13B138 - 178
14X-RAY DIFFRACTION14B179 - 183
15X-RAY DIFFRACTION15B184 - 227
16X-RAY DIFFRACTION16B228 - 266
17X-RAY DIFFRACTION17B267 - 354
18X-RAY DIFFRACTION18B355 - 509
19X-RAY DIFFRACTION19B510 - 524
20X-RAY DIFFRACTION20B525 - 550
21X-RAY DIFFRACTION21C0 - 23
22X-RAY DIFFRACTION22C24 - 100
23X-RAY DIFFRACTION23C101 - 137
24X-RAY DIFFRACTION24C138 - 178
25X-RAY DIFFRACTION25C179 - 192
26X-RAY DIFFRACTION26C193 - 226
27X-RAY DIFFRACTION27C227 - 264
28X-RAY DIFFRACTION28C265 - 354
29X-RAY DIFFRACTION29C355 - 511
30X-RAY DIFFRACTION30C512 - 550
31X-RAY DIFFRACTION31D0 - 45
32X-RAY DIFFRACTION32D46 - 132
33X-RAY DIFFRACTION33D133 - 178
34X-RAY DIFFRACTION34D179 - 227
35X-RAY DIFFRACTION35D228 - 266
36X-RAY DIFFRACTION36D267 - 435
37X-RAY DIFFRACTION37D436 - 450
38X-RAY DIFFRACTION38D451 - 509
39X-RAY DIFFRACTION39D510 - 524
40X-RAY DIFFRACTION40D525 - 550

+
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://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