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- PDB-4wt4: The C-terminal domain of Rubisco Accumulation Factor 1 from Arabi... -

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Basic information

Entry
Database: PDB / ID: 4wt4
TitleThe C-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana, crystal form I
ComponentsRubisco Accumulation Factor 1, isoform 2
KeywordsCHAPERONE
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / chloroplast stroma / chloroplast / cytosol
Similarity search - Function
Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain
Similarity search - Domain/homology
PHOSPHATE ION / Rubisco accumulation factor 1.2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.81 Å
AuthorsHauser, T. / Bhat, J.Y. / Milicic, G. / Wendler, P. / Hartl, F.U. / Bracher, A. / Hayer-Hartl, M.
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Structure and mechanism of the Rubisco-assembly chaperone Raf1.
Authors: Thomas Hauser / Javaid Y Bhat / Goran Miličić / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl /
Abstract: Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation ...Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation factor1 (Raf1), a dimer of ∼40-kDa subunits. We find that Raf1 from Synechococcus elongatus acts downstream of chaperonin-assisted RbcL folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes with four Raf1 dimers bound. Raf1 displacement by RbcS results in holoenzyme formation. Crystal structures show that Raf1 from Arabidopsis thaliana consists of a β-sheet dimerization domain and a flexibly linked α-helical domain. Chemical cross-linking and EM reconstruction indicate that the β-domains bind along the equator of each RbcL2 unit, and the α-helical domains embrace the top and bottom edges of RbcL2. Raf1 fulfills a role similar to that of the assembly chaperone RbcX, thus suggesting that functionally redundant factors ensure efficient Rubisco biogenesis.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rubisco Accumulation Factor 1, isoform 2
B: Rubisco Accumulation Factor 1, isoform 2
C: Rubisco Accumulation Factor 1, isoform 2
D: Rubisco Accumulation Factor 1, isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6437
Polymers75,3584
Non-polymers2853
Water0
1
A: Rubisco Accumulation Factor 1, isoform 2
C: Rubisco Accumulation Factor 1, isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7743
Polymers37,6792
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-27 kcal/mol
Surface area14270 Å2
MethodPISA
2
B: Rubisco Accumulation Factor 1, isoform 2
D: Rubisco Accumulation Factor 1, isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8694
Polymers37,6792
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-37 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.538, 34.361, 106.885
Angle α, β, γ (deg.)90.000, 93.670, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A286 - 435
2010B286 - 435
1020A287 - 436
2020C287 - 436
1030A287 - 434
2030D287 - 434
1040B287 - 435
2040C287 - 435
1050B287 - 434
2050D287 - 434
1060C287 - 433
2060D287 - 433

NCS ensembles :
ID
1
2
3
4
5
6
Detailsbiological unit is a dimer, a.u. contains two dimers

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Components

#1: Protein
Rubisco Accumulation Factor 1, isoform 2


Mass: 18839.576 Da / Num. of mol.: 4 / Fragment: Raf1 beta-domain, UNP residues 281-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAF2, At3g04550, F7O18.2 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SR19
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4

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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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.000041
ReflectionRedundancy: 10.7 % / Number: 94696 / Rsym value: 0.098 / D res high: 3.359 Å / D res low: 43.301 Å / Num. obs: 8850 / % possible obs: 96.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
10.6249.3810.0160.01610.7
7.5110.6210.0240.0249.6
6.137.5110.0680.06810.9
5.316.1310.0920.09211.5
4.755.3110.1070.10710.8
4.344.7510.1280.12810.3
4.014.3410.1980.19811.2
3.754.0110.4430.44311.5
3.543.7510.6020.60211.7
3.363.5411.0991.0997.9
ReflectionResolution: 2.8→45.509 Å / Num. all: 14418 / Num. obs: 14418 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Rsym value: 0.044 / Net I/av σ(I): 15.571 / Net I/σ(I): 20 / Num. measured all: 52140
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.963.50.6971.1706419990.4290.6971.996.5
2.96-3.143.50.3532.2704920060.2170.3533.699.9
3.14-3.353.80.2143.6710918500.1260.2146.3100
3.35-3.623.80.117659817310.0650.1111.799.8
3.62-3.973.70.06911.2590515950.0410.06917.599.6
3.97-4.433.40.03719.9494314500.0230.03729.299.1
4.43-5.123.60.02626.5467012960.0160.02639.399.8
5.12-6.273.70.02528.3411511080.0150.02541.699.9
6.27-8.873.40.01930.429288710.0120.01949.199.4
8.87-45.5093.40.01246.317595120.0080.0126999.1

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.55 / FOM acentric: 0.55 / FOM centric: 0.56 / Reflection: 12877 / Reflection acentric: 11312 / Reflection centric: 1565
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.5-48.7880.950.980.9618426192
5.3-8.50.870.880.7917981498300
4.3-5.30.810.820.721811902279
3.7-4.30.640.650.5622251983242
3.2-3.70.370.380.3138793517362
3-3.20.130.130.1421761986190

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
SHELXphasing
RESOLVE2.13phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 2.81→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2602 / WRfactor Rwork: 0.2162 / FOM work R set: 0.7406 / SU B: 24.625 / SU ML: 0.46 / SU Rfree: 0.473 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2894 717 5 %RANDOM
Rwork0.2399 13676 --
obs0.2423 13676 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 205.89 Å2 / Biso mean: 91.91 Å2 / Biso min: 47.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å2-0 Å2-0.17 Å2
2---3.6 Å2-0 Å2
3---2.08 Å2
Refinement stepCycle: final / Resolution: 2.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 15 0 4458
Biso mean--138.06 --
Num. residues----591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194537
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9866179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5285585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62123.765170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2715745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.971535
X-RAY DIFFRACTIONr_chiral_restr0.0530.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213363
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1430.05
12B1430.05
21A1400.06
22C1400.06
31A1330.06
32D1330.06
41B1380.02
42C1380.02
51B1330.02
52D1330.02
61C1490.01
62D1490.01
LS refinement shellResolution: 2.806→2.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 51 -
Rwork0.372 965 -
all-1016 -
obs--94.16 %

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