[English] 日本語
Yorodumi
- PDB-3moh: The structure of rat cytosolic PEPCK mutant A467G in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3moh
TitleThe structure of rat cytosolic PEPCK mutant A467G in complex with phosphoglycolate and GDP
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis
Function / homology
Function and homology information


Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / cellular hypotonic response / cellular response to fructose stimulus / cellular hypotonic salinity response / glyceraldehyde-3-phosphate biosynthetic process / carboxylic acid binding / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / cellular hyperosmotic response / positive regulation of memory T cell differentiation / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / response to lipid / response to starvation / cellular response to glucagon stimulus / positive regulation of lipid biosynthetic process / cellular response to interleukin-1 / cellular response to retinoic acid / cellular response to cAMP / cellular response to dexamethasone stimulus / response to nutrient levels / response to activity / gluconeogenesis / cellular response to glucose stimulus / response to bacterium / response to insulin / lipid metabolic process / cellular response to insulin stimulus / GDP binding / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / manganese ion binding / cellular response to hypoxia / peptidyl-serine phosphorylation / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / cytosol / cytoplasm
Similarity search - Function
Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / 2-PHOSPHOGLYCOLIC ACID / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsJohnson, T.A. / Holyoak, T.
CitationJournal: Biochemistry / Year: 2010
Title: Increasing the conformational entropy of the Omega-loop lid domain in phosphoenolpyruvate carboxykinase impairs catalysis and decreases catalytic fidelity .
Authors: Johnson, T.A. / Holyoak, T.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_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_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
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
B: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,26215
Polymers139,2602
Non-polymers2,00313
Water12,034668
1
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6628
Polymers69,6301
Non-polymers1,0327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6007
Polymers69,6301
Non-polymers9706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.078, 119.520, 87.018
Angle α, β, γ (deg.)90.000, 107.150, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Phosphoenolpyruvate carboxykinase, cytosolic [GTP] / / PEPCK-C / Phosphoenolpyruvate carboxylase


Mass: 69629.758 Da / Num. of mol.: 2 / Mutation: A467G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: PGEX4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

-
Non-polymers , 7 types, 681 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.22 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion / pH: 7.4
Details: 12-30% PEG 3350, 0.1M HEPES PH 7.4,10 MM MNCL2, 10 MM GDP, hanging drop vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 68897 / % possible obs: 97.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.163 / Χ2: 1.016 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.184.90.73556950.999180.3
2.18-2.265.60.62965421.021193
2.26-2.376.50.54969961.018199.4
2.37-2.497.20.46171060.9831100
2.49-2.657.40.37570431.0281100
2.65-2.857.50.27870611.0031100
2.85-3.147.50.271011.0521100
3.14-3.597.50.136705811100
3.59-4.527.60.09671191.0321100
4.52-1007.60.06771761.02199.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.798 / SU B: 12.334 / SU ML: 0.155 / SU R Cruickshank DPI: 0.272 / SU Rfree: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3483 5.1 %RANDOM
Rwork0.19 ---
obs0.193 68845 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 30.81 Å2 / Biso mean: 12.932 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.02 Å2
2--0.08 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9571 0 99 668 10338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210022
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.97213597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57251245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35924.286448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.279151721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9931559
X-RAY DIFFRACTIONr_chiral_restr0.0970.21424
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217658
X-RAY DIFFRACTIONr_mcbond_it0.5081.56109
X-RAY DIFFRACTIONr_mcangle_it0.8529857
X-RAY DIFFRACTIONr_scbond_it1.64533913
X-RAY DIFFRACTIONr_scangle_it2.4364.53724
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 217 -
Rwork0.282 3656 -
all-3873 -
obs--73.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.70530.8345-0.61394.7911.09164.6883-0.0768-0.0546-0.0725-0.00820.111-0.6138-0.08160.4351-0.03420.0117-0.0158-0.02930.11350.00180.119546.81816.41-3.245
26.8262-2.0020.30777.5947-1.80963.80760.0561-0.01420.60840.1212-0.07720.1247-0.46390.27720.0210.1628-0.0617-0.05660.0905-0.02230.160832.38426.224.983
31.7716-0.645-1.53831.38870.47921.5646-0.00540.09760.03380.0587-0.12510.5558-0.1227-0.11950.13050.05740.0191-0.05140.1068-0.04710.29521.6415.4721.05
46.14214.30410.54413.06710.49192.7696-0.16960.2532-0.1594-0.26570.2055-0.02250.0502-0.0418-0.03590.1939-0.0186-0.0860.10720.00370.06326.015-11.352-14.384
51.18740.6794-0.2582.0608-0.05061.44040.098-0.0169-0.0010.0162-0.0609-0.22940.00920.2661-0.03710.0284-0.0016-0.01860.07090.00130.050438.3488.989-1.781
65.3615-2.11062.61395.1552-2.00185.02470.09470.26990.0888-0.6005-0.09860.10820.09380.00160.00390.0858-0.0356-0.00370.0813-0.0190.009434.26214.431-10.194
70.99241.2391.10915.96610.51373.83870.11310.31630.1532-0.8559-0.40350.4486-0.0399-0.0360.29040.16840.1438-0.04720.22770.0020.031727.60311.3-10.424
81.90.553-1.61242.30930.6674.9807-0.0602-0.0064-0.1220.185-0.04460.00950.01370.01160.10480.0342-0.0188-0.01630.0562-0.0060.032230.9236.619-4.574
93.3974-3.24152.65089.06870.12113.33040.3140.0756-0.1398-0.3803-0.3174-0.20620.05130.35810.00340.0366-0.0545-0.03310.21380.10680.071134.476-6.737-0.295
101.75290.0354-0.35851.11090.57171.6380.0474-0.29940.04680.3728-0.08190.1416-0.0019-0.05390.03440.1752-0.04370.01560.07890.01070.075621.343-5.38118.83
111.0146-0.41770.02692.4556-0.28540.87850.0038-0.18560.09610.3889-0.00080.2785-0.0328-0.0618-0.0030.114-0.04110.0260.1046-0.03250.077720.6158.32114.18
126.49016.1813-2.933526.80941.327211.7560.38540.19540.6781-0.3274-0.59892.8067-1.0591-1.78180.21350.26680.172-0.18080.468-0.05970.56835.31221.3942.008
130.5150.5690.02972.15560.01820.44310.0742-0.09860.04650.3372-0.06540.1065-0.00240.0423-0.00880.1068-0.00280.02450.1115-0.01150.012320.942-4.49313.339
143.20751.7436-1.54212.06630.36272.1231-0.03150.15660.053-0.0460.02350.1771-0.0844-0.05640.0080.0427-0.00630.01030.0293-0.03110.053620.706-13.5590.685
154.0241-1.23070.51853.9707-0.30992.91930.0005-0.0405-0.23660.2876-0.03450.25840.0819-0.11760.0340.109-0.0430.03280.0187-0.00790.030114.869-13.8212.606
161.20240.29810.59041.52880.17372.02290.1133-0.3813-0.11870.5855-0.10770.31550.2036-0.22-0.00560.2476-0.04170.10820.13630.00790.131211.276-15.92122.641
173.215-2.2749-1.92718.962811.896716.8057-0.5091-0.6187-0.29940.5829-0.78311.57870.0127-0.98891.29220.3728-0.04260.24970.3533-0.08310.6019-0.122-16.12415.658
182.4022-1.5775-1.61831.1262-0.13574.1624-0.09430.3656-0.3701-0.0291-0.09970.29510.1346-0.36210.1940.0772-0.049-0.08180.088-0.02320.18513.63-21.237-4.524
1920.4324.3338-3.42576.1292-2.20114.12310.06680.4131-0.4702-0.1917-0.16170.13460.1373-0.21210.09490.1160.0205-0.01640.027-0.0230.105113.182-29.3882.868
206.0539-3.8974-7.37271.36844.03955.8473-0.10190.01880.05760.03480.1128-0.07070.27620.175-0.01090.2511-0.06740.06420.2726-0.06550.254372.19219.20125.638
212.35560.8494-0.9193.67570.54795.0192-0.0239-0.0591-0.0450.14570.0681-0.43470.05850.3639-0.04420.0401-0.0079-0.04370.0725-0.00170.096764.18716.68638.45
221.1893-0.2087-0.23681.9389-0.71851.9530.00830.05530.21780.1958-0.11490.2792-0.3068-0.07730.10660.1856-0.00850.03670.1307-0.02890.178642.70120.66245.734
232.63573.85450.95715.59730.28883.7515-0.06610.1783-0.1122-0.27580.16150.11890.0969-0.1331-0.09540.1775-0.0009-0.05130.1375-0.08260.151643.914-10.01628.963
241.5265.6884-0.242618.17010.36023.6084-0.3080.1246-0.0943-0.96690.2567-0.22930.21640.04510.05130.1039-0.0212-0.03920.1544-0.02780.092750.9543.96223.253
251.85741.2186-0.24612.6773-1.08722.2660.092-0.1217-0.09210.2241-0.1478-0.1670.18680.15450.05570.13590.005-0.02080.0728-0.03790.046158.02210.10643.397
261.59250.0729-0.21412.64050.71632.68790.06790.16670.09060.1424-0.15650.08840.03320.10260.08860.0681-0.04110.02490.0578-0.00760.041652.78512.92638.598
2718.0409-13.9655-0.517517.2060.83175.3872-0.06520.4465-0.03630.07820.0219-0.52280.17540.54750.04330.138-0.05870.01190.13-0.03390.040155.698-1.21832.333
280.66440.356-0.12921.0217-1.24781.35750.0726-0.0588-0.00680.1644-0.00620.0482-0.22420.0113-0.06640.1852-0.0440.01090.0791-0.02710.047545.1-3.31653.165
290.7769-0.42450.60673.58-1.61881.11010.1092-0.16970.01030.6243-0.05560.2122-0.17170.0164-0.05370.2452-0.07450.07140.118-0.04040.080444.4283.51556.66
304.0719-3.7417-1.96043.09312.38712.5752-0.3274-0.0527-0.16990.25680.06960.3834-0.0859-0.09520.25780.33140.0080.19840.1271-0.0250.41529.21620.97254.417
313.47571.3551-0.330212.2052.59319.730.00380.10280.6585-0.3443-0.34972.4534-0.8305-1.79370.34580.30120.11060.0790.4999-0.07270.764623.78720.5546.426
320.02910.5644-0.37891.7433-0.73430.83010.1476-0.04430.02990.2983-0.10150.0573-0.30780.0819-0.04610.2099-0.01640.04230.1261-0.04860.064343.167-1.33656.54
332.11560.9662-1.0971.5165-0.14764.22160.01450.1169-0.0005-0.07960.0210.1555-0.2085-0.2913-0.03560.07780.0008-0.00290.033-0.0130.05833.941-15.12447.936
342.6908-0.92260.66788.831-3.53174.4377-0.02660.1063-0.2688-0.0815-0.00730.0778-0.09580.17580.03390.0637-0.01250.01770.0488-0.0370.047146.205-14.56840.978
352.3527-0.5530.65223.1588-0.25693.56290.1143-0.1531-0.04430.09220.00580.0068-0.2496-0.2203-0.12010.0777-0.02110.00740.07220.00310.036733.592-12.77259.565
360.60580.5121-0.68867.6462.91168.86350.1709-0.4221-0.13610.768-0.41520.62860.0944-0.63440.24430.101-0.07710.00710.37320.07570.203327.779-19.48765.301
372.5032-1.1809-0.56338.0684.502910.50850.1678-0.5194-0.00140.2966-0.28770.86660.1641-0.96550.11990.0463-0.0287-0.01740.31820.01310.276820.894-18.90252.023
380.16061.0229-1.31323.64650.97745.2302-0.1730.2157-0.0843-0.6630.01260.1678-0.0609-0.41410.16050.12170.0003-0.06810.1311-0.06950.14835.687-21.32535.293
3913.03174.5072-2.07725.5448-1.43475.74370.23430.2669-0.3611-0.22450.01840.13650.1798-0.3266-0.25270.05860.008-0.0790.02970.01630.142731.698-29.245.056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 52
2X-RAY DIFFRACTION2A53 - 63
3X-RAY DIFFRACTION3A64 - 94
4X-RAY DIFFRACTION4A95 - 118
5X-RAY DIFFRACTION5A119 - 187
6X-RAY DIFFRACTION6A188 - 204
7X-RAY DIFFRACTION7A205 - 225
8X-RAY DIFFRACTION8A226 - 243
9X-RAY DIFFRACTION9A244 - 259
10X-RAY DIFFRACTION10A260 - 303
11X-RAY DIFFRACTION11A304 - 385
12X-RAY DIFFRACTION12A386 - 398
13X-RAY DIFFRACTION13A399 - 450
14X-RAY DIFFRACTION14A451 - 500
15X-RAY DIFFRACTION15A501 - 525
16X-RAY DIFFRACTION16A526 - 568
17X-RAY DIFFRACTION17A569 - 583
18X-RAY DIFFRACTION18A584 - 606
19X-RAY DIFFRACTION19A607 - 622
20X-RAY DIFFRACTION20B3 - 13
21X-RAY DIFFRACTION21B14 - 54
22X-RAY DIFFRACTION22B55 - 89
23X-RAY DIFFRACTION23B90 - 114
24X-RAY DIFFRACTION24B115 - 133
25X-RAY DIFFRACTION25B134 - 154
26X-RAY DIFFRACTION26B155 - 218
27X-RAY DIFFRACTION27B219 - 227
28X-RAY DIFFRACTION28B228 - 314
29X-RAY DIFFRACTION29B315 - 359
30X-RAY DIFFRACTION30B360 - 387
31X-RAY DIFFRACTION31B388 - 401
32X-RAY DIFFRACTION32B402 - 439
33X-RAY DIFFRACTION33B440 - 482
34X-RAY DIFFRACTION34B483 - 500
35X-RAY DIFFRACTION35B501 - 546
36X-RAY DIFFRACTION36B547 - 571
37X-RAY DIFFRACTION37B572 - 589
38X-RAY DIFFRACTION38B590 - 606
39X-RAY DIFFRACTION39B607 - 622

+
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