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- PDB-8g28: Crystal Structure of the C-terminal Fragment of AAA ATPase from S... -

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Basic information

Entry
Database: PDB / ID: 8g28
TitleCrystal Structure of the C-terminal Fragment of AAA ATPase from Streptococcus pneumoniae.
ComponentsATPase, AAA family
KeywordsHYDROLASE / Center for Structural Biology of Infectious Diseases (CSBID) / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / AAA ATPase
Function / homology
Function and homology information


DNA replication / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
MgsA AAA+ ATPase C-terminal / AAA C-terminal domain / : / MgsA AAA+ ATPase C terminal / AAA C-terminal domain / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal Structure of the C-terminal Fragment of AAA ATPase from Streptococcus pneumoniae.
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase, AAA family
B: ATPase, AAA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4493
Polymers95,4142
Non-polymers351
Water5,765320
1
A: ATPase, AAA family
B: ATPase, AAA family
hetero molecules

A: ATPase, AAA family
B: ATPase, AAA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,8986
Polymers190,8274
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area8140 Å2
ΔGint-80 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.532, 71.532, 151.435
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-731-

HOH

21A-744-

HOH

31B-653-

HOH

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Components

#1: Protein ATPase, AAA family


Mass: 47706.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was hydrolyzed during the crystallization experiment.
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: SP_1790 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 Magic / References: UniProt: A0A0H2URL5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 5.6 mg/ml, 0.25M Sodium chloride, 0.01M Tris pH 8.3; Screen: Classics II (F12), 0.2M Sodium chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2021
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 57219 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 24.4 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.017 / Rrim(I) all: 0.084 / Rsym value: 0.082 / Χ2: 1.085 / Net I/σ(I): 42.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 21.1 % / Rmerge(I) obs: 1.512 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2800 / CC1/2: 0.731 / CC star: 0.919 / Rpim(I) all: 0.331 / Rsym value: 1.512 / Χ2: 1.005 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→29.18 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.12 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.143 2879 5.1 %RANDOM
Rwork0.1202 ---
obs0.1213 54123 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.3 Å2 / Biso mean: 16.748 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å2-0 Å2
2---0.03 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.3→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 2 372 1962
Biso mean--23.46 31.42 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131933
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151903
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.6382650
X-RAY DIFFRACTIONr_angle_other_deg0.3461.5844401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3375266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.35521.53891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94315331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8471515
X-RAY DIFFRACTIONr_chiral_restr0.0650.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0580.022283
X-RAY DIFFRACTIONr_gen_planes_other0.0530.02419
X-RAY DIFFRACTIONr_rigid_bond_restr0.78533836
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 217 -
Rwork0.234 3895 -
all-4112 -
obs--99.98 %
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)
14.69442.1974-0.98941.6049-1.55552.3096-0.02480.0847-0.2034-0.1377-0.0307-0.08940.27540.16470.05550.08050.05220.02360.08050.00930.082965.6548.49113.016
25.44482.32960.56586.326-1.73232.5057-0.0227-0.35490.06560.0901-0.1052-0.36690.09820.3290.12790.01330.0326-0.01290.12110.00150.072468.93611.66621.056
32.8104-0.82460.79571.27620.60483.6022-0.05720.0010.09570.00630.0992-0.22390.00030.3496-0.0420.0025-0.00090.00010.0469-0.00150.052564.89618.25710.432
41.54021.11770.72971.88851.3983.1547-0.0128-0.04010.0615-0.025-0.0149-0.0473-0.05070.00840.02770.00340.0014-0.00190.01430.00980.028455.70521.81411.541
50.59370.0015-0.15910.42260.3091.7091-0.0164-0.0715-0.02410.00810.0299-0.09120.05360.0964-0.01350.0198-0.0014-0.00540.03130.00870.046659.20617.3514.532
61.15510.6075-3.4611.1471-1.683710.415-0.05360.05060.0078-0.0960.07950.05330.1457-0.0761-0.02590.0753-0.01270.01520.2056-0.02210.054661.97217.475-16.032
73.6658-0.4382-1.17572.40070.32.01170.11330.38390.115-0.2201-0.09060.0761-0.0334-0.1035-0.02260.02580.0021-0.00620.10290.02190.009952.00128.142-12.932
812.2722.21770.21394.37481.5282.37570.02150.3050.1441-0.07190.0659-0.1945-0.1456-0.1116-0.08750.01980.00290.01590.06460.01560.031962.92526.65-11.954
93.1428-0.8928-1.01041.73880.29620.99790.05010.1310.1359-0.0936-0.0273-0.0957-0.0657-0.022-0.02290.0125-0.00510.00850.02470.01140.027453.20934.44-3.573
103.1648-1.5876-0.47941.20930.51950.6685-0.1162-0.08910.06020.03260.1087-0.0348-0.05610.08910.00760.0176-0.0050.00850.04050.00330.04757.2728.0453.752
111.3636-1.40650.00971.88070.16720.4751-0.00630.0904-0.0607-0.0587-0.02860.0668-0.05710.01410.03490.0179-0.0140.00170.02750.00230.024449.42129.118-3.11
126.1343-1.31422.854614.64072.32534.3903-0.06220.1410.3537-0.97440.04190.0689-0.50590.06440.02030.2353-0.0225-0.0230.01420.02310.05140.33653.586-4.092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 258
2X-RAY DIFFRACTION2A259 - 270
3X-RAY DIFFRACTION3A271 - 285
4X-RAY DIFFRACTION4A286 - 305
5X-RAY DIFFRACTION5A306 - 337
6X-RAY DIFFRACTION6A338 - 345
7X-RAY DIFFRACTION7B241 - 261
8X-RAY DIFFRACTION8B262 - 269
9X-RAY DIFFRACTION9B270 - 289
10X-RAY DIFFRACTION10B290 - 311
11X-RAY DIFFRACTION11B312 - 337
12X-RAY DIFFRACTION12B338 - 344

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