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- PDB-2e9x: The crystal structure of human GINS core complex -

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Basic information

Entry
Database: PDB / ID: 2e9x
TitleThe crystal structure of human GINS core complex
Components
  • (DNA replication complex GINS protein ...) x 2
  • (GINS complex subunit ...) x 2
KeywordsREPLICATION / GINS complex / Eukaryotic DNA replication
Function / homology
Function and homology information


Unwinding of DNA / DNA strand elongation involved in mitotic DNA replication / GINS complex / CMG complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / inner cell mass cell proliferation / DNA unwinding involved in DNA replication / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1020 / Ribosomal Protein L9; domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2050 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1030 / Ribosomal Protein L9; domain 1 - #50 / Ribosomal Protein L9; domain 1 / GINS/PriA/YqbF domain / DNA replication complex GINS protein Psf2 / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1020 / Ribosomal Protein L9; domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2050 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1030 / Ribosomal Protein L9; domain 1 - #50 / Ribosomal Protein L9; domain 1 / GINS/PriA/YqbF domain / DNA replication complex GINS protein Psf2 / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / GINS complex, subunit Psf3 superfamily / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein helical bundle domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA replication complex GINS protein PSF1 / DNA replication complex GINS protein SLD5 / DNA replication complex GINS protein PSF3 / DNA replication complex GINS protein PSF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKamada, K. / Hanaoka, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structure of the human GINS complex and its assembly and functional interface in replication initiation
Authors: Kamada, K. / Kubota, Y. / Arata, T. / Shindo, Y. / Hanaoka, F.
History
DepositionJan 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: DNA replication complex GINS protein PSF1
B: DNA replication complex GINS protein PSF2
C: GINS complex subunit 3
D: GINS complex subunit 4
E: DNA replication complex GINS protein PSF1
F: DNA replication complex GINS protein PSF2
G: GINS complex subunit 3
H: GINS complex subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,36214
Polymers179,7858
Non-polymers5766
Water9,584532
1
A: DNA replication complex GINS protein PSF1
B: DNA replication complex GINS protein PSF2
C: GINS complex subunit 3
D: GINS complex subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1817
Polymers89,8934
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15100 Å2
ΔGint-151 kcal/mol
Surface area32320 Å2
MethodPISA
2
E: DNA replication complex GINS protein PSF1
F: DNA replication complex GINS protein PSF2
G: GINS complex subunit 3
H: GINS complex subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1817
Polymers89,8934
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-135 kcal/mol
Surface area32080 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32310 Å2
ΔGint-293 kcal/mol
Surface area61770 Å2
MethodPISA
4
A: DNA replication complex GINS protein PSF1
B: DNA replication complex GINS protein PSF2
C: GINS complex subunit 3
D: GINS complex subunit 4
hetero molecules

E: DNA replication complex GINS protein PSF1
F: DNA replication complex GINS protein PSF2
G: GINS complex subunit 3
H: GINS complex subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,36214
Polymers179,7858
Non-polymers5766
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area32270 Å2
ΔGint-302 kcal/mol
Surface area61810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.928, 88.741, 102.129
Angle α, β, γ (deg.)104.689, 102.964, 95.467
Int Tables number1
Space group name H-MP1

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Components

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DNA replication complex GINS protein ... , 2 types, 4 molecules AEBF

#1: Protein DNA replication complex GINS protein PSF1


Mass: 17502.084 Da / Num. of mol.: 2 / Fragment: C-terminal truncation, residues 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Gene: PSF1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14691
#2: Protein DNA replication complex GINS protein PSF2


Mass: 21453.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Gene: PSF2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y248

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GINS complex subunit ... , 2 types, 4 molecules CGDH

#3: Protein GINS complex subunit 3


Mass: 24854.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Gene: psf3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BRX5
#4: Protein GINS complex subunit 4


Mass: 26081.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Gene: sld5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BRT9

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Non-polymers , 2 types, 538 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Na malonate-HCl, 1M LiSO4, 0.5M (NH4)2SO4, 20mM DTT, 0.1%(v/v) isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-5A20.97951, 0.97930, 0.97488, 0.98332
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDOct 14, 2004Collimating and Focusing mirrors
ADSC QUANTUM 3152CCDOct 14, 2004Collimating and Focusing mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Numerical link type Si(111) double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Numerical link type Si(111) double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979511
30.97931
40.974881
50.983321
Reflection

D res high: 2.3 Å / D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
2112.53014250.0481.2415400991.5
2213.63013110.0461.3715374591.4
1.9311.43025810.0531.2615518091.6
1.9410.62949820.051.0315226289.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955098.110.0362.0982
3.934.9598.210.0351.8082
3.443.9398.410.0381.52
3.123.4498.110.0491.2452
2.93.1298.110.0651.0582
2.732.99810.0950.9782
2.592.7397.810.1240.92
2.482.5997.310.1560.8671.9
2.382.4874.710.1720.8111.9
2.32.385610.2070.791.9
4.95509820.0362.3632
3.934.9598.220.0362.0462
3.443.9398.320.0371.682
3.123.4498.120.0461.3892
2.93.129820.061.192
2.732.998.120.0811.0242
2.592.7397.820.1020.9392
2.482.5997.120.1250.9031.9
2.382.487420.140.8721.9
2.32.3856.220.170.8271.9
4.955097.930.0382.2662
3.934.9598.130.0361.8382
3.443.9398.230.0411.5592
3.123.4498.130.0551.2252
2.93.1298.230.081.0622
2.732.99830.1190.9482
2.592.7397.830.1630.8862
2.482.5997.330.2040.8271.9
2.382.4877.230.2290.8161.8
2.32.385530.2620.7691.8
4.955098.440.0321.5812
3.934.9598.340.0321.3332
3.443.9398.440.0381.1492
3.123.4498.140.0591.012
2.93.1298.140.0940.9362
2.732.997.940.150.8462
2.592.7397.740.2110.7992
2.482.5995.740.2660.7851.9
2.382.4867.340.2860.7571.8
2.32.3845.740.3210.7121.7
ReflectionResolution: 1.99→50 Å / Num. all: 101605 / Num. obs: 101605 / % possible obs: 78.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 28.3 Å2 / Limit h max: 28 / Limit h min: -29 / Limit k max: 43 / Limit k min: -29 / Limit l max: 45 / Limit l min: 0 / Observed criterion F max: 1761658.59 / Observed criterion F min: 13.1 / Rsym value: 0.047 / Χ2: 1.209 / Net I/σ(I): 21.01
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3669 / Rsym value: 0.341 / Χ2: 0.947 / % possible all: 28.2

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.3 Å / D res low: 47.67 Å / FOM : 0 / FOM acentric: 0.485 / FOM centric: 0 / Reflection: 0 / Reflection acentric: 78117 / Reflection centric: 0
Phasing MAD set

R cullis centric: 0 / Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Loc centric: 0 / Power centric: 0 / Reflection centric: _

IDR cullis acentricLoc acentricPower acentricReflection acentric
12.040.1078117
20.9913.10.2277970
30.8911.20.8378005
40.915.60.7577276
Phasing MAD set shell

R cullis centric: 0 / Loc centric: 0 / Power centric: 0 / Reflection centric: _

IDResolution (Å)R cullis acentricLoc acentricPower acentricReflection acentric
113.75-47.673.940.30377
18.04-13.751.230.101580
15.68-8.041.850.103635
14.39-5.681.310.106519
13.58-4.391.270.1010233
13.02-3.581.80.1014780
12.61-3.022.850.1020079
12.3-2.613.470.1020914
213.75-47.670.9822.30.21376
28.04-13.750.9723.50.191579
25.68-8.040.9718.50.233634
24.39-5.680.9918.70.26517
23.58-4.390.9917.20.210228
23.02-3.580.9913.30.2214773
22.61-3.020.9910.50.2420075
22.3-2.6119.80.2120788
313.75-47.670.8423.80.68375
38.04-13.750.8219.10.771579
35.68-8.040.7712.91.053633
34.39-5.680.8212.40.996515
33.58-4.390.8612.70.8910231
33.02-3.580.8710.70.914779
32.61-3.020.929.90.8220075
32.3-2.610.9710.40.6520818
413.75-47.670.8123.70.86376
48.04-13.750.84200.921580
45.68-8.040.8215.71.093635
44.39-5.680.8618.20.856519
43.58-4.390.8819.90.7210230
43.02-3.580.89160.7614776
42.61-3.020.9213.30.7720067
42.3-2.610.95140.6120093
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1ano20-0.425-0.426-0.3680
2ano20-0.793-0.27-0.8750
3ano20-0.754-0.84-0.2790
4ano20-0.375-0.825-0.9630
5ano20-0.182-0.737-0.8730
6ano20-0.768-0.155-0.5190
7ano20-0.849-0.023-0.8180
8ano20-0.289-0.574-0.3870
9ano20-0.347-0.719-0.8040
10ano20-0.951-0.14-0.8550
11ano20-0.697-0.066-0.3030
12ano20-0.76-0.926-0.4420
13ano20-0.685-0.777-0.3690
14ano20-0.686-0.728-0.9450
15ano20-0.931-0.302-0.6940
16ano20-0.796-0.851-0.3930
17ano20-0.907-0.349-0.6880
18ano20-0.691-0.552-0.7120
19ano20-0.666-0.74-0.3070
20ano20-0.132-0.548-0.4220
21ano20-0.804-0.927-0.70
22ano20-0.704-0.84-0.6430
23ano20-0.683-0.604-0.5450
24ano20-0.436-0.562-0.6550
25ano20-0.977-0.692-0.4340
26ano20-0.119-0.62-0.5480
27ano20-0.019-0.594-0.5990
28ano20-0.05-0.909-0.8240
29ano20-0.884-0.113-0.0270
30ano20-0.683-0.234-0.5310
31ano20-0.287-0.784-0.8510
32ano20-0.844-0.265-0.9020
33ano20-0.372-0.59-0.7860
34ano20-0.151-0.773-0.8680
35ano20-0.019-0.408-0.1780
36ano20-0.659-0.974-0.4720
37ano20-0.43-0.432-0.3731.189
38ano20-0.801-0.269-0.8771.071
39ano20-0.754-0.854-0.2770.909
40ano20-0.386-0.824-0.9681.425
41ano20-0.183-0.741-0.8691.15
42ano20-0.803-0.108-0.5260.359
43ano20-0.856-0.028-0.8261.365
44ano20-0.285-0.585-0.3911.199
45ano20-0.374-0.715-0.8120.388
46ano20-0.949-0.139-0.8710.715
47ano20-0.706-0.075-0.3120.516
48ano20-0.759-0.943-0.4430.288
49ano20-0.709-0.781-0.3731.023
50ano20-0.703-0.729-0.9530.789
51ano20-0.926-0.322-0.6890.903
52ano20-0.774-1.011-0.5250.052
53ano20-0.904-0.358-0.7010.251
54ano20-0.682-0.56-0.7190.742
55ano20-0.662-0.75-0.310.458
56ano20-0.137-0.557-0.4241.098
57ano20-0.816-0.915-0.6940.523
58ano20-0.728-0.836-0.6440.77
59ano20-0.697-0.621-0.560.827
60ano20-0.455-0.578-0.6590.553
61ano20-0.977-0.702-0.4361.133
62ano20-0.128-0.627-0.5531.431
63ano20-0.036-0.611-0.6050.864
64ano20-0.056-0.917-0.8271.28
65ano20-0.884-0.117-0.031.124
66ano20-0.705-0.218-0.5360.629
67ano20-0.318-0.798-0.8580.291
68ano20-0.748-0.323-0.9520.014
69ano20-0.377-0.596-0.7851.404
70ano20-0.172-0.774-0.8640.326
71ano20-0.024-0.433-0.1730.552
72ano20-0.669-0.975-0.480.607
73ano20-0.427-0.426-0.3674.697
74ano20-0.795-0.273-0.8774.007
75ano20-0.754-0.837-0.2823.989
76ano20-0.363-0.825-0.9582.715
77ano20-0.181-0.739-0.8773.615
78ano20-0.77-0.158-0.523.968
79ano20-0.846-0.024-0.8122.959
80ano20-0.292-0.571-0.3843.551
81ano20-0.345-0.72-0.8033.546
82ano20-0.951-0.14-0.8533.076
83ano20-0.688-0.065-0.2992.762
84ano20-0.76-0.925-0.4412.941
85ano20-0.679-0.775-0.3683.295
86ano20-0.679-0.726-0.9392.66
87ano20-0.929-0.3-0.6943.231
88ano20-0.797-0.853-0.393.002
89ano20-0.909-0.348-0.6873.569
90ano20-0.697-0.548-0.7123.455
91ano20-0.671-0.742-0.3061.867
92ano20-0.13-0.544-0.4242.033
93ano20-0.802-0.93-0.7021.682
94ano20-0.696-0.841-0.6423.411
95ano20-0.685-0.602-0.5442.923
96ano20-0.432-0.56-0.6553.38
97ano20-0.982-0.683-0.4342.855
98ano20-0.113-0.61-0.5451.306
99ano20-0.013-0.59-0.5962.712
100ano20-0.044-0.901-0.8242.278
101ano20-0.887-0.107-0.0251.267
102ano20-0.681-0.237-0.5313.088
103ano20-0.289-0.785-0.8522.733
104ano20-0.852-0.269-0.9043.241
105ano20-0.353-0.577-0.791.785
106ano20-0.145-0.773-0.8682.258
107ano20-0.013-0.407-0.1840.857
108ano20-0.658-0.978-0.4651.978
109ano20-0.426-0.425-0.3664.898
110ano20-0.793-0.274-0.8774.453
111ano20-0.754-0.836-0.2824.72
112ano20-0.36-0.825-0.9563.293
113ano20-0.18-0.739-0.8783.973
114ano20-0.77-0.157-0.5194.939
115ano20-0.845-0.022-0.813.552
116ano20-0.292-0.571-0.3834.498
117ano20-0.343-0.719-0.8024.139
118ano20-0.95-0.14-0.8523.957
119ano20-0.685-0.064-0.2973.691
120ano20-0.758-0.924-0.4393.546
121ano20-0.676-0.774-0.3664.226
122ano20-0.677-0.725-0.9383.325
123ano20-0.928-0.299-0.6954.148
124ano20-0.796-0.853-0.3893.948
125ano20-0.909-0.348-0.6864.516
126ano20-0.697-0.547-0.7114.223
127ano20-0.673-0.741-0.3052.034
128ano20-0.128-0.542-0.4232.376
129ano20-0.8-0.929-0.72.163
130ano20-0.695-0.841-0.6424.407
131ano20-0.685-0.601-0.5433.707
132ano20-0.431-0.558-0.6554.542
133ano20-0.981-0.682-0.4333.857
134ano20-0.112-0.607-0.5451.489
135ano20-0.013-0.589-0.5953.682
136ano20-0.043-0.898-0.8232.733
137ano20-0.889-0.105-0.0241.558
138ano20-0.68-0.236-0.533.846
139ano20-0.288-0.784-0.8523.264
140ano20-0.852-0.268-0.9044.198
141ano20-0.353-0.576-0.7892.527
142ano20-0.145-0.773-0.8693.074
143ano20-0.016-0.408-0.1841.254
144ano20-0.656-0.978-0.4642.085
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
13.75-47.6700.53807579323483770
8.04-13.7500.6120129691374715800
5.68-8.0400.6790159968928136350
4.39-5.6800.631075945120565190
3.58-4.3900.5960792477229102330
3.02-3.5800.55301414418246147800
2.61-3.0200.45101110391870200790
2.3-2.6100.32501291848254209140
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 78115
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
12.47-100600.562511
8.82-12.4749.90.874971
7.2-8.8253.40.8581243
6.23-7.256.60.8381489
5.58-6.2358.50.8271683
5.09-5.58530.8411865
4.71-5.0954.90.8582024
4.41-4.7153.40.8442137
4.16-4.4152.60.8512325
3.94-4.1656.40.8352451
3.76-3.9456.10.8162547
3.6-3.7657.20.812702
3.46-3.656.30.8112792
3.33-3.4657.80.82897
3.22-3.3364.60.7252964
3.12-3.2268.40.73128
3.02-3.1268.30.7093179
2.94-3.0268.20.7083288
2.86-2.9470.60.6933380
2.79-2.8670.30.6743459
2.72-2.7971.50.6493584
2.66-2.7272.20.6663602
2.6-2.6671.80.6533753
2.54-2.672.50.6593760
2.49-2.5473.60.6343878
2.45-2.4975.20.6353574
2.4-2.4575.30.6282990
2.36-2.475.20.6272673
2.3-2.3680.60.5893266

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM4.2phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.82 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 4042 4.9 %random
Rwork0.197 ---
all0.199 81853 --
obs0.199 81768 97.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 36.5066 Å2 / ksol: 0.364426 e/Å3
Displacement parametersBiso max: 95.23 Å2 / Biso mean: 35.59 Å2 / Biso min: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å22.93 Å22.08 Å2
2---5.96 Å2-1.34 Å2
3---2.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11413 0 30 535 11978
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4661.5
X-RAY DIFFRACTIONc_mcangle_it2.3952
X-RAY DIFFRACTIONc_scbond_it2.3482
X-RAY DIFFRACTIONc_scangle_it3.482.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.2544284.60.21788520.01210536928088.1
2.4-2.530.2654964.80.21297940.012105091029097.9
2.53-2.690.2575275.10.20797620.011105011028998
2.69-2.90.2785375.20.21998550.012105571039298.4
2.9-3.190.2564834.70.21298470.012104681033098.7
3.19-3.650.235295.10.19798920.01105401042198.9
3.65-4.60.19351950.1798760.008104771039599.2
4.6-29.820.22552350.19399320.01105171045599.4

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