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- PDB-2py8: RbcX -

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Basic information

Entry
Database: PDB / ID: 2py8
TitleRbcX
ComponentsHypothetical protein rbcX
KeywordsCHAPERONE / All helical fold
Function / homologyChaperonin-like RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsTanaka, S. / Sawaya, M.R. / Kerfeld, C.A. / Yeates, T.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803.
Authors: Tanaka, S. / Sawaya, M.R. / Kerfeld, C.A. / Yeates, T.O.
History
DepositionMay 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein rbcX
B: Hypothetical protein rbcX
C: Hypothetical protein rbcX
D: Hypothetical protein rbcX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5538
Polymers66,4544
Non-polymers1,0994
Water1,56787
1
B: Hypothetical protein rbcX
C: Hypothetical protein rbcX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9364
Polymers33,2272
Non-polymers7092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-26 kcal/mol
Surface area14120 Å2
MethodPISA, PQS
2
A: Hypothetical protein rbcX
hetero molecules

A: Hypothetical protein rbcX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2984
Polymers33,2272
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4660 Å2
ΔGint-27 kcal/mol
Surface area14150 Å2
MethodPISA, PQS
3
D: Hypothetical protein rbcX
hetero molecules

D: Hypothetical protein rbcX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9364
Polymers33,2272
Non-polymers7092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4830 Å2
ΔGint-15 kcal/mol
Surface area11610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.832, 129.832, 92.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-601-

PE4

21B-618-

HOH

DetailsThe chain B and chain C form a dimer, and the chain A and chain D form another dimer.

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Components

#1: Protein
Hypothetical protein rbcX


Mass: 16613.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC6803 / Gene: rbcX / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q55670
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 30% PEG 400, 0.1M potassium/sodium phosphate, 0.2M lithium sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97947,0.97969,0.97182
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979471
20.979691
30.971821
Reflection

D res high: 3.3 Å / D res low: 90 Å / % possible obs: 100

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs
7.4111.31683670.0941.0922720
6.829.5844520.1061.0412475
7.4310.41703530.11.0922996
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.119099.810.0481.0517.7
5.647.1110010.0771.0477.6
4.935.6410010.0811.0667.1
4.484.9310010.0811.0087.3
4.164.4810010.1091.0677.4
3.914.1610010.151.0897.4
3.723.9110010.2021.1227.4
3.553.7210010.2541.1557.4
3.423.5510010.3181.1717.4
3.33.4210010.491.1627.4
7.119099.920.0571.0676.4
5.647.1110020.0851.0786.8
4.935.6410020.091.0356.5
4.484.9399.920.091.0266.7
4.164.4810020.1231.0886.9
3.914.1610020.1681.0056.9
3.723.9110020.2311.0546.9
3.553.7210020.2851.0326.9
3.423.5510020.3721.0526.9
3.33.4210020.5720.9456.9
7.119099.930.0491.1137.7
5.647.1110030.081.0237.6
4.935.6410030.0851.0527.1
4.484.9310030.0840.9777.3
4.164.4810030.1171.0987.4
3.914.1610030.1671.087.4
3.723.9110030.2321.1447.4
3.553.7210030.2951.1467.4
3.423.5510030.3921.1977.4
3.33.4210030.6111.0827.4
ReflectionResolution: 2.45→90 Å / Num. all: 29666 / Num. obs: 29666 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Χ2: 1.038 / Net I/σ(I): 16.7
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.541 / Num. unique all: 2896 / Χ2: 1.032 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 3.3 Å / D res low: 20 Å / FOM : 0.327 / FOM acentric: 0.34 / FOM centric: 0.257 / Reflection: 12359 / Reflection acentric: 10357 / Reflection centric: 2002
Phasing MAD set

Highest resolution: 3.3 Å / Lowest resolution: 20 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
10.970.9211.215.70.480.37103552002
20.980.9611.617.20.430.31102901997
32.1410000103572002
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
112.25-200.850.741416.60.960.7212891
18.83-12.250.880.7512.415.50.960.76308136
16.9-8.830.870.819.912.31.040.75561180
15.67-6.90.910.868.711.71.010.65899233
14.8-5.670.960.928.713.70.780.461314273
14.17-4.80.991.019.813.90.550.331802314
13.68-4.170.99111.616.70.330.22372366
13.3-3.680.990.9913.621.20.210.122971409
212.25-200.90.8514.118.30.790.5412891
28.83-12.250.960.8912.319.60.810.51308136
26.9-8.830.930.9510.614.80.840.54561180
25.67-6.90.950.929.714.60.790.46899233
24.8-5.670.970.961014.50.620.41314273
24.17-4.80.980.9710.5160.480.281802314
23.68-4.170.990.9911.6180.330.182373366
23.3-3.680.990.9913.620.50.230.132905404
312.25-201.091000012891
38.83-12.251.1310000308136
36.9-8.831.5310000561180
35.67-6.94.2410000899233
34.8-5.672.32100001314273
34.17-4.81.76100001802314
33.68-4.172.18100002373366
33.3-3.682.65100002972409
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se62.6840.7050.190.0540.094
2Se71.0080.7240.3320.0320.092
3Se91.5030.6910.7480.0780.085
4Se86.9980.6170.3480.0880.057
5Se118.1370.8160.1780.0860.056
6Se53.5260.7050.190.0530.082
7Se55.2130.7240.3320.0320.073
8Se69.7110.6910.7480.0780.066
9Se87.0720.6180.3470.0890.045
10Se100.1730.8160.1780.0870.044
11Se52.760.7050.190.0540
12Se56.4210.7240.3320.0310
13Se73.7560.6910.7480.0770
14Se66.2280.6190.3470.090
15Se89.4260.8160.180.0870
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.25-200.5720.6570.45321912891
8.83-12.250.5630.5990.482444308136
6.9-8.830.6120.6630.455741561180
5.67-6.90.5670.6130.3931132899233
4.8-5.670.4610.4930.30815871314273
4.17-4.80.3450.370.20521161802314
3.68-4.170.2220.2370.12327392373366
3.3-3.680.1470.1540.133812972409
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 29549
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.53-10024.70.891510
7.63-9.5326.50.905512
6.62-7.6328.70.891558
5.92-6.62330.87616
5.41-5.9232.40.883685
5.01-5.41300.9731
4.69-5.0130.10.913787
4.42-4.6928.30.896826
4.19-4.4231.60.89867
4-4.19340.858920
3.83-440.60.818956
3.68-3.8340.10.839999
3.55-3.6842.20.8351004
3.43-3.5542.20.8031076
3.32-3.4346.10.7971100
3.22-3.3282.70.6951137
3.13-3.2290.70.6911161
3.04-3.1386.80.6931205
2.97-3.0490.60.7081213
2.9-2.9789.50.6861238
2.83-2.990.20.6921292
2.77-2.8391.30.7031309
2.71-2.77890.711321
2.65-2.7191.40.6861368
2.6-2.6591.70.6821386
2.55-2.689.40.6571425
2.51-2.5590.10.6481432
2.45-2.5190.50.5111915

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.45→19.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.571 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1495 5.1 %RANDOM
Rwork0.209 ---
obs0.211 29544 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.617 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 54 87 3827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213792
X-RAY DIFFRACTIONr_bond_other_d0.0010.022542
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.975131
X-RAY DIFFRACTIONr_angle_other_deg0.87836225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1325456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81224.545187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08715671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5881530
X-RAY DIFFRACTIONr_chiral_restr0.0630.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
X-RAY DIFFRACTIONr_nbd_refined0.2140.2967
X-RAY DIFFRACTIONr_nbd_other0.1720.22419
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21832
X-RAY DIFFRACTIONr_nbtor_other0.0860.22013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.216
X-RAY DIFFRACTIONr_mcbond_it3.67722498
X-RAY DIFFRACTIONr_mcbond_other1.0472914
X-RAY DIFFRACTIONr_mcangle_it4.73933727
X-RAY DIFFRACTIONr_scbond_it3.82121582
X-RAY DIFFRACTIONr_scangle_it5.36631404
LS refinement shellResolution: 2.451→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 95 -
Rwork0.301 1995 -
obs-2090 99.05 %
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)
12.6217-2.3533-3.72912.52953.25015.3267-0.38040.0851-0.17230.53290.19890.0420.61280.36550.1815-0.1963-0.02510.0286-0.2172-0.0891-0.40547.58641.22948.235
26.48330.75591.27351.2008-0.10031.7335-0.00030.3221-0.46090.0680.0906-0.03490.19630.1317-0.0903-0.31240.07770.0553-0.11790.0609-0.398239.96291.22361.016
33.50760.37620.5340.9132-0.06421.2279-0.14240.45220.41160.06420.09110.1434-0.0833-0.00650.0513-0.31330.08230.0127-0.19840.0742-0.350334.63999.33461.852
46.7978-1.56832.0545.9986-1.238610.51640.19540.18441.1206-0.5790.2939-0.5265-1.31510.1367-0.48930.2138-0.1630.3281-0.2289-0.0521-0.24351.18862.25542.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1202 - 120
2X-RAY DIFFRACTION2BB2 - 1152 - 115
3X-RAY DIFFRACTION3CC2 - 1232 - 123
4X-RAY DIFFRACTION4DD2 - 1042 - 104

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