[English] 日本語
Yorodumi
- PDB-5bsh: Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Car... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bsh
TitleCrystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase (MtP5CR) in complex with L-Proline
ComponentsPyrroline-5-carboxylate reductase
KeywordsOXIDOREDUCTASE / proline biosynthesis / decamer / P5C / plant protein
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / nucleotide binding
Similarity search - Function
ProC C-terminal domain-like / ProC C-terminal domain-like fold / : / Delta 1-pyrroline-5-carboxylate reductase signature. / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...ProC C-terminal domain-like / ProC C-terminal domain-like fold / : / Delta 1-pyrroline-5-carboxylate reductase signature. / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROLINE / Pyrroline-5-carboxylate reductase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRuszkowski, M. / Nocek, B. / Forlani, G. / Dauter, Z.
Citation
Journal: Front Plant Sci / Year: 2015
Title: The structure of Medicago truncatula delta (1)-pyrroline-5-carboxylate reductase provides new insights into regulation of proline biosynthesis in plants.
Authors: Ruszkowski, M. / Nocek, B. / Forlani, G. / Dauter, Z.
#1: Journal: J. Mol. Biol. / Year: 2005
Title: Crystal structures of delta1-pyrroline-5-carboxylate reductase from human pathogens Neisseria meningitides and Streptococcus pyogenes.
Authors: Nocek, B. / Chang, C. / Li, H. / Lezondra, L. / Holzle, D. / Collart, F. / Joachimiak, A.
#2: Journal: New Phytol. / Year: 2014
Title: (delta)1-Pyrroline-5-carboxylate reductase from Arabidopsis thaliana: stimulation or inhibition by chloride ions and feedback regulation by proline depend on whether NADPH or NADH acts as co-substrate.
Authors: Giberti, S. / Funck, D. / Forlani, G.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyrroline-5-carboxylate reductase
B: Pyrroline-5-carboxylate reductase
C: Pyrroline-5-carboxylate reductase
D: Pyrroline-5-carboxylate reductase
E: Pyrroline-5-carboxylate reductase
F: Pyrroline-5-carboxylate reductase
G: Pyrroline-5-carboxylate reductase
H: Pyrroline-5-carboxylate reductase
I: Pyrroline-5-carboxylate reductase
J: Pyrroline-5-carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,03220
Polymers287,88110
Non-polymers1,15110
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54520 Å2
ΔGint-534 kcal/mol
Surface area93150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.489, 100.928, 101.925
Angle α, β, γ (deg.)67.650, 85.460, 89.440
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILESERSERAA3 - 2746 - 277
21ILEILESERSERBB3 - 2746 - 277
12PROPROSERSERAA5 - 2748 - 277
22PROPROSERSERCC5 - 2748 - 277
13PROPROSERSERAA5 - 2748 - 277
23PROPROSERSERDD5 - 2748 - 277
14ILEILESERSERAA3 - 2746 - 277
24ILEILESERSEREE3 - 2746 - 277
15ILEILESERSERAA3 - 2746 - 277
25ILEILESERSERFF3 - 2746 - 277
16PROPROSERSERAA7 - 27410 - 277
26PROPROSERSERGG7 - 27410 - 277
17ILEILESERSERAA3 - 2746 - 277
27ILEILESERSERHH3 - 2746 - 277
18PROPROLEULEUAA5 - 2738 - 276
28PROPROLEULEUII5 - 2738 - 276
19ILEILELEULEUAA4 - 2737 - 276
29ILEILELEULEUJJ4 - 2737 - 276
110PROPROSERSERBB5 - 2748 - 277
210PROPROSERSERCC5 - 2748 - 277
111PROPROSERSERBB5 - 2748 - 277
211PROPROSERSERDD5 - 2748 - 277
112ILEILESERSERBB3 - 2746 - 277
212ILEILESERSEREE3 - 2746 - 277
113ILEILESERSERBB3 - 2746 - 277
213ILEILESERSERFF3 - 2746 - 277
114PROPROSERSERBB7 - 27410 - 277
214PROPROSERSERGG7 - 27410 - 277
115ILEILESERSERBB3 - 2746 - 277
215ILEILESERSERHH3 - 2746 - 277
116PROPROLEULEUBB5 - 2738 - 276
216PROPROLEULEUII5 - 2738 - 276
117ILEILELEULEUBB4 - 2737 - 276
217ILEILELEULEUJJ4 - 2737 - 276
118PROPROSERSERCC5 - 2748 - 277
218PROPROSERSERDD5 - 2748 - 277
119PROPROSERSERCC5 - 2748 - 277
219PROPROSERSEREE5 - 2748 - 277
120PROPROSERSERCC5 - 2748 - 277
220PROPROSERSERFF5 - 2748 - 277
121PROPROSERSERCC7 - 27410 - 277
221PROPROSERSERGG7 - 27410 - 277
122PROPROSERSERCC5 - 2748 - 277
222PROPROSERSERHH5 - 2748 - 277
123PROPROSERSERCC5 - 2748 - 277
223PROPROSERSERII5 - 2748 - 277
124PROPROSERSERCC5 - 2748 - 277
224PROPROSERSERJJ5 - 2748 - 277
125PROPROSERSERDD5 - 2748 - 277
225PROPROSERSEREE5 - 2748 - 277
126PROPROSERSERDD5 - 2748 - 277
226PROPROSERSERFF5 - 2748 - 277
127PROPROSERSERDD7 - 27410 - 277
227PROPROSERSERGG7 - 27410 - 277
128PROPROSERSERDD5 - 2748 - 277
228PROPROSERSERHH5 - 2748 - 277
129PROPROSERSERDD5 - 2748 - 277
229PROPROSERSERII5 - 2748 - 277
130PROPROSERSERDD5 - 2748 - 277
230PROPROSERSERJJ5 - 2748 - 277
131ILEILESERSEREE3 - 2746 - 277
231ILEILESERSERFF3 - 2746 - 277
132PROPROSERSEREE7 - 27410 - 277
232PROPROSERSERGG7 - 27410 - 277
133ILEILESERSEREE3 - 2746 - 277
233ILEILESERSERHH3 - 2746 - 277
134PROPROLEULEUEE5 - 2738 - 276
234PROPROLEULEUII5 - 2738 - 276
135ILEILELEULEUEE4 - 2737 - 276
235ILEILELEULEUJJ4 - 2737 - 276
136PROPROSERSERFF7 - 27410 - 277
236PROPROSERSERGG7 - 27410 - 277
137ILEILESERSERFF3 - 2746 - 277
237ILEILESERSERHH3 - 2746 - 277
138PROPROLEULEUFF5 - 2738 - 276
238PROPROLEULEUII5 - 2738 - 276
139ILEILELEULEUFF4 - 2737 - 276
239ILEILELEULEUJJ4 - 2737 - 276
140PROPROSERSERGG7 - 27410 - 277
240PROPROSERSERHH7 - 27410 - 277
141PROPROSERSERGG7 - 27410 - 277
241PROPROSERSERII7 - 27410 - 277
142PROPROSERSERGG7 - 27410 - 277
242PROPROSERSERJJ7 - 27410 - 277
143PROPROLEULEUHH5 - 2738 - 276
243PROPROLEULEUII5 - 2738 - 276
144ILEILELEULEUHH4 - 2737 - 276
244ILEILELEULEUJJ4 - 2737 - 276
145PROPROLEULEUII5 - 2738 - 276
245PROPROLEULEUJJ5 - 2738 - 276

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

-
Components

#1: Protein
Pyrroline-5-carboxylate reductase


Mass: 28788.066 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_7g090160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3)
References: UniProt: G7KRM5, pyrroline-5-carboxylate reductase
#2: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Morpheus screen (Molecular Dimensions) A7 solution (100 mM HEPES/MOPS buffer pH 7.5, 10% polyethylene glycol 4000, 20% glycerol, 30 mM MgCl2 and 30 mM CaCl2).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 183949 / % possible obs: 97.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.05 / Rrim(I) all: 0.086 / Χ2: 1.265 / Net I/av σ(I): 13.352 / Net I/σ(I): 9 / Num. measured all: 481562
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.60.4821.991120.7750.3650.6080.76696.7
2.14-2.182.60.43191250.7990.3250.5430.79496.8
2.18-2.222.60.34891620.870.2630.4390.84896.9
2.22-2.262.60.391360.8910.2260.3770.87597.1
2.26-2.312.60.26391610.9160.1990.3320.89697.2
2.31-2.372.60.23391480.9310.1750.2930.9397.3
2.37-2.422.60.20291550.9440.1510.2531.02797.3
2.42-2.492.60.17391670.9560.130.2181.06897.6
2.49-2.562.60.15592170.9620.1150.1941.15697.7
2.56-2.652.60.13291660.9750.0980.1661.24497.8
2.65-2.742.60.11493020.980.0840.1421.29498
2.74-2.852.60.10391700.9820.0750.1281.5198
2.85-2.982.60.09692660.9840.070.121.71798.2
2.98-3.142.60.08692580.9850.0620.1061.72798.3
3.14-3.332.60.0892620.9850.0580.0991.8698.5
3.33-3.592.60.07692800.9860.0550.0942.02798.5
3.59-3.952.60.0793010.9880.050.0861.60698.8
3.95-4.522.60.06392940.990.0450.0781.53698.9
4.52-5.72.60.05593390.9920.0390.0681.39699.1
5.7-402.70.04789280.9930.0340.0590.93294.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZZ, 5BSE

2izz

5bse


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.2145 / WRfactor Rwork: 0.1959 / FOM work R set: 0.8035 / SU ML: 0.13 / SU Rfree: 0.1411 / Cross valid method: FREE R-VALUE / ESU R: 0.174 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1941 1.1 %RANDOM
Rwork0.18 ---
obs0.18 182006 97 %-
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 max: 260.65 Å2 / Biso mean: 74 Å2 / Biso min: 35.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0.4 Å2-1.78 Å2
2--1.6 Å21.54 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19678 0 80 695 20453
Biso mean--76.58 57.07 -
Num. residues----2700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01920298
X-RAY DIFFRACTIONr_bond_other_d0.010.0220294
X-RAY DIFFRACTIONr_angle_refined_deg1.61.98227498
X-RAY DIFFRACTIONr_angle_other_deg1.365346760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78252737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90824.267675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86153499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.42315110
X-RAY DIFFRACTIONr_chiral_restr0.0860.23272
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02122990
X-RAY DIFFRACTIONr_gen_planes_other0.0090.024114
X-RAY DIFFRACTIONr_mcbond_it4.1113.89910942
X-RAY DIFFRACTIONr_mcbond_other4.1043.89810941
X-RAY DIFFRACTIONr_mcangle_it5.6475.80813681
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A158700.06
12B158700.06
21A156240.04
22C156240.04
31A155540.05
32D155540.05
41A157500.07
42E157500.07
51A159460.05
52F159460.05
61A151650.06
62G151650.06
71A159270.05
72H159270.05
81A156440.06
82I156440.06
91A156830.06
92J156830.06
101B155210.06
102C155210.06
111B155400.05
112D155400.05
121B158510.07
122E158510.07
131B159360.06
132F159360.06
141B151190.06
142G151190.06
151B159660.05
152H159660.05
161B156650.06
162I156650.06
171B157010.06
172J157010.06
181C155300.05
182D155300.05
191C154080.07
192E154080.07
201C156040.04
202F156040.04
211C151350.06
212G151350.06
221C155610.05
222H155610.05
231C155450.05
232I155450.05
241C154940.06
242J154940.06
251D153420.07
252E153420.07
261D155060.05
262F155060.05
271D150800.06
272G150800.06
281D154910.05
282H154910.05
291D154810.05
292I154810.05
301D154210.06
302J154210.06
311E158830.06
312F158830.06
321E149980.08
322G149980.08
331E158350.07
332H158350.07
341E155420.07
342I155420.07
351E155550.08
352J155550.08
361F151790.06
362G151790.06
371F159760.05
372H159760.05
381F157280.05
382I157280.05
391F157290.06
392J157290.06
401G150920.06
402H150920.06
411G150590.06
412I150590.06
421G150190.07
422J150190.07
431H156850.05
432I156850.05
441H157300.05
442J157300.05
451I156620.05
452J156620.05
LS refinement shellResolution: 2.1→2.15 Å
RfactorNum. reflection% reflection
Rfree0.269 115 -
Rwork0.268 12189 -
obs--87.69 %
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)
11.4463-0.0201-0.37590.04660.15582.27520.2097-0.04050.07980.03510.1062-0.0439-0.13710.0043-0.31590.39180.02050.02710.2249-0.03060.278868.75270.04890.5173
20.7726-0.01880.14460.3372-0.26270.27690.0558-0.1436-0.1346-0.03490.06980.0073-0.0242-0.0214-0.12560.3631-0.06710.00360.2345-0.00290.304648.898861.32667.7445
31.7222-0.49510.32321.4388-1.41961.46630.0377-0.185-0.1932-0.15830.35630.34820.1354-0.2786-0.39410.2656-0.1536-0.10550.38010.2110.365725.112644.136880.8333
40.8323-0.12270.25620.13520.03530.27380.0315-0.1237-0.1473-0.03960.09160.0148-0.055-0.0412-0.1230.3689-0.0570.00390.24530.01680.281746.739663.622368.3334
52.2865-0.91561.08121.9499-0.43230.6185-0.02650.25720.3770.1636-0.3144-0.2406-0.18090.08470.34090.5513-0.0336-0.04760.0881-0.03060.365158.4808112.006367.5828
61.16510.05490.15010.1644-0.25680.50880.0153-0.01550.08510.0510.0264-0.0334-0.0567-0.093-0.04170.3716-0.01350.07740.2344-0.02580.288242.264586.191459.8443
70.57810.1416-0.09980.71581.57233.81610.513-0.27750.0620.1504-0.4612-0.06940.0678-1.0334-0.05180.4406-0.10020.1330.82160.06070.164912.187491.299569.8723
80.88120.15790.32220.4602-0.38050.58650.0076-0.00190.08450.07190.03650.0157-0.043-0.0824-0.04410.3755-0.00610.07880.223-0.02760.296540.885187.393657.239
91.08860.31660.51230.7424-0.56941.18580.05460.0798-0.032-0.0578-0.0805-0.1132-0.04180.0130.0260.29360.03270.0970.25580.07530.315568.3554105.172519.3749
100.63210.13950.19760.27240.10860.2163-0.00910.15250.02290.06210.0150.0176-0.00690.0488-0.00590.30130.03460.06170.32250.01670.271945.677287.50833.2113
111.9414-0.27990.38962.7840.1220.10710.11550.18690.20960.1276-0.20870.46320.05620.09670.09320.20390.02390.05980.36120.03610.312717.31897.031921.4357
120.76650.31330.0190.1904-0.10850.4341-0.01610.16060.01980.05010.01670.0646-0.00840.0506-0.00060.28540.02980.06610.33710.00840.264345.286485.469730.7531
130.06-0.1217-0.09467.00743.83972.1363-0.080.1244-0.0831-0.27411.499-2.6277-0.1540.7192-1.4190.1019-0.12280.23150.847-0.88861.275482.368458.251611.9826
140.23470.03110.05810.3931-0.01520.1660.02960.1786-0.00040.03640.0707-0.12060.047-0.0367-0.10030.29420.04810.030.3933-0.12770.259554.185963.445924.4695
152.01471.0642-0.59590.67890.13152.0198-0.01540.04210.6005-0.03490.00550.37390.1254-0.0240.00990.30090.1132-0.06520.2701-0.15980.327732.533254.19832.3667
160.340.19780.16480.48030.21840.21460.05340.204-0.04330.05540.0637-0.07910.06110.0078-0.11710.27790.05960.03550.4035-0.13850.252153.610560.436325.374
173.2560.22730.83961.1105-1.34982.02881.1525-0.0157-1.16460.5039-0.58450.084-0.23170.6868-0.5680.602-0.213-0.36920.271-0.03150.742482.877836.849558.4184
180.90950.27450.12960.1081-0.00840.56040.20710.137-0.35360.0463-0.0164-0.0582-0.02510.054-0.19070.33510.0264-0.08560.1573-0.15020.422356.163847.270645.9885
192.0042-0.5269-0.82333.82411.08030.5472-0.11560.5347-0.05260.14250.15240.04730.1161-0.1554-0.03680.3224-0.0662-0.39560.17580.03770.558537.57222.680538.5799
200.7472-0.11060.15460.0816-0.17210.49330.21860.0443-0.34920.0136-0.01820.0307-0.0377-0.015-0.20040.33470.008-0.11750.1366-0.10660.466454.531946.951848.7407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 169
2X-RAY DIFFRACTION2A170 - 274
3X-RAY DIFFRACTION3B3 - 169
4X-RAY DIFFRACTION4B170 - 274
5X-RAY DIFFRACTION5C5 - 169
6X-RAY DIFFRACTION6C170 - 274
7X-RAY DIFFRACTION7D5 - 169
8X-RAY DIFFRACTION8D170 - 274
9X-RAY DIFFRACTION9E3 - 169
10X-RAY DIFFRACTION10E170 - 274
11X-RAY DIFFRACTION11F3 - 169
12X-RAY DIFFRACTION12F170 - 274
13X-RAY DIFFRACTION13G7 - 169
14X-RAY DIFFRACTION14G170 - 274
15X-RAY DIFFRACTION15H3 - 169
16X-RAY DIFFRACTION16H170 - 274
17X-RAY DIFFRACTION17I5 - 169
18X-RAY DIFFRACTION18I170 - 274
19X-RAY DIFFRACTION19J4 - 169
20X-RAY DIFFRACTION20J170 - 274

+
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