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- PDB-3zc4: The structure of Csa5 from Sulfolobus solfataricus. -

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Basic information

Entry
Database: PDB / ID: 3zc4
TitleThe structure of Csa5 from Sulfolobus solfataricus.
ComponentsSSO1398
KeywordsIMMUNE SYSTEM / CAS
Function / homology
Function and homology information


defense response to virus
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1610 / SH3 type barrels. - #1260 / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / CRISPR type I-A cluster 1/Apern-associated protein Csa5-1
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å
AuthorsReeks, J. / Anderson, L. / White, M.F. / Naismith, J.H.
CitationJournal: RNA Biol. / Year: 2013
Title: Structure of the Archaeal Cascade Subunit Csa5: Relating the Small Subunits of Crispr Effector Complexes.
Authors: Reeks, J. / Graham, S. / Anderson, L. / Liu, H. / White, M.F. / Naismith, J.H.
History
DepositionNov 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Jul 31, 2013Group: Atomic model / Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SSO1398
B: SSO1398
C: SSO1398
D: SSO1398
E: SSO1398
F: SSO1398
G: SSO1398
H: SSO1398
I: SSO1398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,84218
Polymers168,8879
Non-polymers9559
Water2,882160
1
A: SSO1398


Theoretical massNumber of molelcules
Total (without water)18,7651
Polymers18,7651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SSO1398


Theoretical massNumber of molelcules
Total (without water)18,7651
Polymers18,7651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SSO1398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8712
Polymers18,7651
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SSO1398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8712
Polymers18,7651
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SSO1398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8712
Polymers18,7651
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: SSO1398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8712
Polymers18,7651
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: SSO1398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8712
Polymers18,7651
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: SSO1398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9773
Polymers18,7651
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: SSO1398
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9773
Polymers18,7651
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)285.000, 53.720, 216.680
Angle α, β, γ (deg.)90.00, 124.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
SSO1398


Mass: 18765.188 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: Q97YC8
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.99 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 4
Details: 0.1 M SODIUM ACETATE PH 4.0, 0.23 M POTASSIUM CHLORIDE AND 39 % PEG500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9787
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.72→59.42 Å / Num. obs: 73275 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.3
Reflection shellResolution: 2.72→2.8 Å / Redundancy: 7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
xia2data scaling
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.72→58.61 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.91 / SU B: 19.221 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED DURING REFINEMENT. THE COMMAND NCSR LOCAL WAS USED AS PART OF REFMAC V 5.6.0117.
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 3691 5 %RANDOM
Rwork0.20473 ---
obs0.20535 69581 99.92 %-
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: 36.782 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.46 Å2
2--0.27 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.72→58.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11311 0 63 160 11534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211647
X-RAY DIFFRACTIONr_bond_other_d0.0040.028143
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.98515796
X-RAY DIFFRACTIONr_angle_other_deg1.0943.00219801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96851388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2223.191492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.876152003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7391581
X-RAY DIFFRACTIONr_chiral_restr0.0630.21814
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112508
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022409
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.725→2.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 246 -
Rwork0.304 4850 -
obs--99.98 %
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)
124.00642.19385.979823.12053.389325.3024-0.57431.041.7895-1.8002-0.1402-0.1557-1.51730.89450.71450.2766-0.0497-0.11710.49930.04190.2464.5378-36.2046252.2097
22.20150.54020.48250.99190.14113.3286-0.0365-0.4431-0.00670.15020.02620.29320.0131-0.24160.01030.113-0.0359-0.00950.33890.05530.18380.6169-49.0799262.1221
316.4206-1.1376-6.46624.5825-3.27765.6483-0.44890.5899-0.5918-1.05540.0977-0.15561.1501-0.24920.35110.50710.1306-0.19460.6442-0.1170.344116.9939-60.3924250.5247
43.5012-1.8240.97596.42311.39363.86920.2081-0.0058-0.0615-0.3411-0.05-0.0187-0.03550.2214-0.15810.0719-0.04520.00460.33760.07930.04386.0963-48.8658254.4735
529.7671-7.996925.27052.7858-9.278731.5097-1.20851.05282.6952-0.5375-0.1209-0.56122.15830.24491.32941.3643-0.0953-0.14570.78850.1480.5709-2.1871-42.4184230.521
63.5622-0.24190.98451.5364-0.3413.7063-0.0231-0.4480.0190.13480.03210.1881-0.028-0.2866-0.00890.1752-0.0373-0.08570.29960.02550.2393-12.8165-49.0609243.1185
78.4766-0.775-0.22817.42.74737.10760.70251.198-1.3545-0.3744-0.113-0.23960.91180.0376-0.58950.57570.0169-0.32320.37910.01910.6112-8.3928-68.5733234.1306
84.26881.9041.69336.11220.33053.98580.11630.0695-0.4242-0.44840.0556-0.24580.36870.1785-0.1720.21750.0392-0.08390.26310.04920.1228-8.9841-53.7915234.9569
918.18721.8714-3.02483.5715-1.93279.01140.07280.4209-0.1717-0.2503-0.2406-0.59430.21120.62760.16780.31920.0557-0.12240.10050.04670.2209-20.8878-44.7357215.7875
103.3519-0.1750.89084.3637-1.21394.15410.1717-0.1948-0.11470.1964-0.08740.29040.1729-0.5558-0.08430.21250.0387-0.07930.30740.04790.1722-28.2887-47.4277222.8636
116.90621.62481.12911.0347-2.00794.97980.24370.2499-0.9318-0.20370.010.19790.8605-0.4067-0.25370.3832-0.0702-0.16280.28610.02760.2186-34.165-54.4567214.6174
127.75281.30871.25795.1315-2.54525.204-0.11310.18190.00690.0642-0.0494-0.4286-0.04520.5220.16250.28540.096-0.08190.1698-0.00690.1151-16.2354-42.7898217.9831
138.0538-0.28650.24133.8556-1.42262.421-0.0676-0.1328-0.156-0.0104-0.1107-0.39470.1550.47640.17830.22910.0349-0.04940.12480.06040.1362-27.6854-29.7852201.0916
149.11350.89657.19973.4511.97056.1786-0.1763-0.82280.20510.473-0.0570.17550.082-0.60220.23320.24260.0824-0.01910.16720.0240.0841-39.7428-35.7356210.0032
158.29333.06614.28461.16631.5722.2247-0.0858-0.04340.1356-0.02020.02520.1532-0.1193-0.0390.06060.44270.09660.04590.20290.01180.3339-52.4402-35.0831199.4836
166.1876-0.8943-0.47143.3566-0.9833.66790.01580.0576-0.30520.1124-0.04850.01450.1376-0.02660.03270.19240.0392-0.03740.0115-0.01090.0224-36.3874-33.588199.2678
177.53844.2657-10.90199.53591.176324.451-0.35310.6615-0.5551-0.98390.0664-0.3278-0.0145-1.01020.28670.24830.118-0.01320.1636-0.10220.3851-32.181-25.4784175.0544
181.5361.20970.43523.1974-1.215.7816-0.0922-0.3041-0.01820.3841-0.0999-0.4401-0.09250.30440.19210.15840.0572-0.04620.1308-0.03270.1798-29.3046-15.2819188.4863
1910.1056-1.59562.11970.88620.65442.0112-0.37830.08230.183-0.23360.06640.1965-0.57780.11040.31190.28130.01390.02220.09510.12470.3236-51.8722-7.7971183.3248
204.5318-2.2973-0.71375.8568-0.70253.84840.0910.0946-0.1733-0.00310.01730.14260.026-0.1529-0.10830.0401-0.0155-0.00220.01430.00040.0118-37.8726-15.5536181.8951
2117.843812.3368-5.64321.51985.367237.3486-0.26121.2397-0.191-1.5492-0.26090.27050.6422-2.48440.5220.32110.01150.08530.28830.01130.3524-33.6908-11.7502156.6268
223.81090.6686-1.40821.0364-0.3624.22930.0318-0.0892-0.2250.1027-0.0987-0.34720.1510.4690.0670.1038-0.00450.05180.06130.01130.2251-22.1724-6.1298168.4039
2321.6546-5.37365.56623.80060.91144.1229-0.29341.13141.19250.408-0.26140.355-0.29040.31680.55480.5613-0.0040.36720.07960.01870.5465-36.197613.2068167.8276
242.00830.2764-0.8158.50070.51683.81620.11370.00720.1376-0.3618-0.03420.2435-0.2539-0.0823-0.07950.0373-0.00220.01410.0244-0.00580.101-30.0789-0.1462163.4498
2524.61466.66787.27168.104913.90851.9695-0.71210.8988-0.1022-0.4858-0.1380.7302-0.508-1.64850.85010.30130.01410.15820.27970.03150.3146-28.65-0.6693137.9397
262.0196-1.098-0.24892.13710.38583.9622-0.0949-0.0874-0.0151-0.00380.0621-0.07030.10190.39360.03280.1683-0.04120.110.1522-0.00220.2405-14.4335-0.6182147.6456
277.0447-8.14232.136613.8958-1.08962.02510.41331.0120.8398-0.2556-0.6588-0.0086-0.94871.03920.24551.377-0.58440.41490.5831-0.04760.5647-12.8420.2641143.6831
285.06472.7752-0.70555.43050.47624.5052-0.05140.20120.501-0.28430.07670.2752-0.5190.0891-0.02540.21840.02390.05760.11610.02390.1515-18.22836.0399142.128
2916.5197-6.366916.92877.17517.753860.5798-0.96091.76760.08310.3052-1.06410.639-1.31960.46622.02490.51140.00260.17850.68550.08960.4177-21.18852.8678116.0907
302.74560.8609-0.43671.00931.10254.49360.0734-0.047-0.14160.34460.00190.14620.39090.144-0.07530.22090.02110.09310.33490.00170.2303-11.4884-8.4322124.1861
314.6118-1.2833-2.82324.84733.0295.38570.2569-0.09540.6418-0.19690.0575-0.7268-0.66851.0867-0.31440.3246-0.16980.09520.6302-0.0240.36272.54496.5267124.6153
326.97550.2895-1.45041.7610.51434.53250.04330.25630.58950.03180.14520.1082-0.47560.2831-0.18850.2918-0.02720.06390.26870.060.1335-7.99941.9516119.4765
3315.5774-0.664229.949414.88854.325759.72610.23530.46150.4814-1.1066-1.40520.8243-0.09390.33211.16990.4884-0.05720.15360.6881-0.00330.3991-15.4821-0.782494.1985
340.68540.892-0.50212.1265-0.00583.16140.0195-0.2697-0.03370.3364-0.06040.14780.1447-0.07970.04080.20280.0120.04230.40640.02620.1836-9.663-14.1031104.0198
359.74352.5311-1.38288.3961-2.79242.5679-0.08450.7666-0.0052-1.04410.6395-0.54440.64010.5749-0.5550.30090.007-0.07970.7471-0.27240.43129.7919-11.709793.3913
365.8762-1.391-0.12412.43940.97093.47780.14620.2680.3173-0.0058-0.0194-0.0411-0.12960.2085-0.12670.1598-0.07160.01290.31440.07160.0852-5.601-9.621297.0411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 18
2X-RAY DIFFRACTION2A19 - 70
3X-RAY DIFFRACTION3A71 - 91
4X-RAY DIFFRACTION4A92 - 162
5X-RAY DIFFRACTION5B6 - 16
6X-RAY DIFFRACTION6B17 - 67
7X-RAY DIFFRACTION7B68 - 91
8X-RAY DIFFRACTION8B92 - 162
9X-RAY DIFFRACTION9C6 - 29
10X-RAY DIFFRACTION10C30 - 94
11X-RAY DIFFRACTION11C95 - 125
12X-RAY DIFFRACTION12C126 - 162
13X-RAY DIFFRACTION13D6 - 50
14X-RAY DIFFRACTION14D51 - 71
15X-RAY DIFFRACTION15D72 - 92
16X-RAY DIFFRACTION16D93 - 162
17X-RAY DIFFRACTION17E5 - 18
18X-RAY DIFFRACTION18E19 - 66
19X-RAY DIFFRACTION19E67 - 92
20X-RAY DIFFRACTION20E93 - 162
21X-RAY DIFFRACTION21F6 - 16
22X-RAY DIFFRACTION22F17 - 63
23X-RAY DIFFRACTION23F64 - 91
24X-RAY DIFFRACTION24F92 - 162
25X-RAY DIFFRACTION25G6 - 17
26X-RAY DIFFRACTION26G18 - 70
27X-RAY DIFFRACTION27G71 - 92
28X-RAY DIFFRACTION28G93 - 162
29X-RAY DIFFRACTION29H6 - 16
30X-RAY DIFFRACTION30H17 - 55
31X-RAY DIFFRACTION31H56 - 92
32X-RAY DIFFRACTION32H93 - 162
33X-RAY DIFFRACTION33I6 - 16
34X-RAY DIFFRACTION34I17 - 70
35X-RAY DIFFRACTION35I71 - 92
36X-RAY DIFFRACTION36I93 - 162

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