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- PDB-3thg: Crystal structure of the creosote Rubisco activase C-domain -

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Basic information

Entry
Database: PDB / ID: 3thg
TitleCrystal structure of the creosote Rubisco activase C-domain
ComponentsRibulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic
KeywordsPROTEIN BINDING / Four-helix bundle / Rubisco reactivation / Chloroplast Stroma / AAA+ / ATPase
Function / homology
Function and homology information


chloroplast stroma / ATP binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1070 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic
Similarity search - Component
Biological speciesLarrea tridentata (creosote bush)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å
AuthorsHenderson, J.N. / Kuriata, A.M. / Fromme, R. / Salvucci, M.E. / Wachter, R.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Atomic resolution x-ray structure of the substrate recognition domain of higher plant ribulose-bisphosphate carboxylase/oxygenase (Rubisco) activase.
Authors: Henderson, J.N. / Kuriata, A.M. / Fromme, R. / Salvucci, M.E. / Wachter, R.M.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1152
Polymers12,0231
Non-polymers921
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic
hetero molecules

A: Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2294
Polymers24,0452
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556-x+2/3,-x+y+1/3,-z+4/31
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.919, 71.919, 151.698
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic / RA 1 / RuBisCO activase 1 / RuBisCO activase alpha form


Mass: 12022.628 Da / Num. of mol.: 1 / Fragment: unp residues 308-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Larrea tridentata (creosote bush) / Gene: RCA1 / Plasmid: pET151-DTOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*(DE3) / References: UniProt: Q7X9A0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE DEPOSITED SEQUENCE UNP Q7X9A0 IS WRONG AT THE POSITION H354

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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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.2 M trimethylamine N-oxide, 20% PEG MME 2000, pH 8.5, vapor diffusion, hanging drop, temperature 283K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97921
2
3
4
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 16, 2011
2CCD
3CCD
4CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionRedundancy: 9.9 % / Av σ(I) over netI: 4.28 / Number: 54867 / Rmerge(I) obs: 0.063 / Rsym value: 0.092 / D res high: 1.88 Å / Num. obs: 8910 / % possible obs: 37.6
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
8.4148.1322681.60.0390.03310.6
5.958.4147699.60.0380.05313.8
4.865.956391000.0510.09815.9
4.214.8674199.90.050.19317.5
3.764.2182999.90.0550.27412.3
3.443.7694399.90.0620.0517.3
3.183.4410291000.0720.0757.3
2.973.1810791000.1090.137.3
2.82.9711611000.1520.2267.3
2.662.812171000.2270.5367.2
2.542.6657043.80.304
2.432.54
2.332.43
2.252.33
2.172.25
2.12.17
2.042.1
1.982.04
1.931.98
1.881.93
ReflectionResolution: 1.88→48.135 Å / Num. all: 12496 / Num. obs: 12496 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rsym value: 0.092 / Net I/σ(I): 22.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.88-1.987.20.5361.40.536197.2
1.98-2.17.30.2263.30.2261100
2.1-2.257.30.135.70.131100
2.25-2.437.30.0759.70.0751100
2.43-2.667.30.05113.20.0511100
2.66-2.9812.30.2741.50.274199.9
2.98-3.4417.50.1932.70.1931100
3.44-4.2115.90.0986.30.0981100
4.21-5.9513.80.053110.0531100
5.95-48.13510.60.03314.50.033199.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XSCALEdata scaling
SHELXDphasing
RefinementResolution: 1.88→48.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0 / SU B: 7.204 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1251 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23803 606 4.9 %RANDOM
Rwork0.21595 ---
obs0.21691 11875 99.55 %-
all-12496 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.88→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 6 42 828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022766
X-RAY DIFFRACTIONr_bond_other_d0.0030.02552
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9691037
X-RAY DIFFRACTIONr_angle_other_deg0.99331318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00823.7532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41915123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.394156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02158
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_it1.7081.5494
X-RAY DIFFRACTIONr_mcbond_other0.5691.5207
X-RAY DIFFRACTIONr_mcangle_it2.6492791
X-RAY DIFFRACTIONr_scbond_it3.8133272
X-RAY DIFFRACTIONr_scangle_it5.7364.5244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.884→1.932 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 44 -
Rwork0.37 812 -
obs--95.86 %
Refinement TLS params.Method: refined / Origin x: 4.732 Å / Origin y: 28.307 Å / Origin z: 88.663 Å
111213212223313233
T0.2053 Å2-0.0242 Å2-0.0329 Å2-0.2152 Å2-0.0612 Å2--0.2706 Å2
L5.8976 °23.5577 °23.968 °2-3.6919 °23.196 °2--5.471 °2
S0.0898 Å °0.6206 Å °-0.4375 Å °-0.2914 Å °0.2974 Å °-0.3022 Å °0.395 Å °0.2643 Å °-0.3872 Å °

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