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- PDB-7yil: The structure of GINS from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 7yil
TitleThe structure of GINS from Methanocaldococcus jannaschii
ComponentsGINS
KeywordsDNA BINDING PROTEIN / GINS / CMG complex / helicase
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #1030 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / Uncharacterized protein MJ0248
Function and homology information
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsWang, W.W. / Liu, X.P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170097 China
National Natural Science Foundation of China (NSFC)U1832161 China
National Natural Science Foundation of China (NSFC)41921006 China
CitationJournal: To Be Published
Title: The structure of GINS from Methanocaldococcus jannaschii
Authors: Wang, W.W. / Yi, G.S. / Zhou, H. / Zhao, Y.X. / Wang, Q.S. / He, J.H. / Yu, F. / Xiao, X. / Liu, X.P.
History
DepositionJul 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GINS
B: GINS


Theoretical massNumber of molelcules
Total (without water)23,6252
Polymers23,6252
Non-polymers00
Water30617
1
A: GINS

A: GINS

A: GINS

A: GINS


Theoretical massNumber of molelcules
Total (without water)47,2504
Polymers47,2504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area7480 Å2
ΔGint-49 kcal/mol
Surface area19820 Å2
MethodPISA
2
B: GINS

B: GINS

B: GINS

B: GINS


Theoretical massNumber of molelcules
Total (without water)47,2504
Polymers47,2504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_555-y,-x,-z+1/31
Buried area7360 Å2
ΔGint-50 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.410, 67.410, 236.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein GINS


Mass: 11812.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: MJ0248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57698
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20.1% PEG 1500, 5.36% MPD, 0.1M Tris-Base pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.17→33.79 Å / Num. obs: 17808 / % possible obs: 99.7 % / Redundancy: 35.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.013 / Rrim(I) all: 0.079 / Net I/σ(I): 26.7 / Num. measured all: 638608 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.17-2.2330.51.5763871812690.8940.2871.6032.599.7
9.71-33.7925.20.04866852650.9990.0090.04953.997.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GHS and 2E9X

5ghs

2e9x


Resolution: 2.17→32.67 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 912 5.14 %
Rwork0.2168 16821 -
obs0.2183 17733 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.42 Å2 / Biso mean: 73.7196 Å2 / Biso min: 40.76 Å2
Refinement stepCycle: final / Resolution: 2.17→32.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 0 17 1650
Biso mean---60.94 -
Num. residues----186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.280.33241390.278623052444100
2.28-2.430.25491130.24762357247099
2.43-2.610.26421350.241123372472100
2.61-2.880.33871200.256723632483100
2.88-3.290.26521350.25723832518100
3.29-4.150.26261230.210724582581100
4.15-32.670.21171470.19492618276599
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)
11.9635-2.64480.26469.1001-1.08882.0409-0.3706-0.2893-0.95141.00830.67021.2221-0.1013-1.2821-0.18170.85140.02620.18950.99630.08060.810617.4526-10.122620.2284
27.7111-1.74756.03227.79070.43678.63560.530.3531-0.6429-0.37160.09440.91460.9135-0.4474-0.49690.6036-0.06230.09670.84210.06210.624219.9931-10.35619.8646
35.55962.951-0.26485.8681.18696.7685-0.27-0.22780.20090.38710.26220.73940.0252-0.77340.00080.41940.07890.06650.58090.01720.42622.1954-2.533816.3486
44.48464.17760.58127.32762.4842.1764-0.0984-0.2042-0.10970.5665-0.5957-1.63291.80721.45830.42990.84280.2684-0.02310.85870.02130.898135.9138-13.225116.528
52.18420.7923-3.42913.78471.06058.86270.1090.93160.4745-0.02370.56030.0286-0.30590.2689-0.38980.36550.0799-0.01320.90920.03360.501841.185-1.37894.0705
66.751-0.39310.24913.9340.693.64190.18660.21810.7221-0.4283-0.0604-0.3822-0.20021.0334-0.19050.5755-0.02630.1330.92380.06390.535121.46159.745827.4025
71.21781.0627-1.1484.9309-0.13174.37850.0546-0.131-0.03650.2118-0.0737-0.59710.29590.53330.00290.35560.13210.00230.6742-0.01210.519618.49923.699935.0743
85.4344-1.1284-0.44111.25911.65683.01770.24660.83680.482-0.3309-0.0958-0.0093-0.2905-0.5945-0.16430.53570.1925-0.05780.6913-0.00070.5352-0.222310.362433.5905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 38 )A24 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 62 )A39 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 86 )A63 - 86
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 95 )A87 - 95
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 115 )A96 - 115
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 48 )B21 - 48
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 86 )B49 - 86
8X-RAY DIFFRACTION8chain 'B' and (resid 87 through 114 )B87 - 114

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