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- PDB-5bs2: Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii in c... -

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Basic information

Entry
Database: PDB / ID: 5bs2
TitleCrystal structure of RbcX-IIa from Chlamydomonas reinhardtii in complex with RbcL C-terminal tail
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase large chain,CrRbcX-IIa
KeywordsCHAPERONE / RbcX
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / carbon fixation / photosynthesis / protein folding chaperone / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Chaperonin-like RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal ...Chaperonin-like RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Predicted protein / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsBracher, A. / Hauser, T. / Liu, C. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Plos One / Year: 2015
Title: Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii.
Authors: Bracher, A. / Hauser, T. / Liu, C. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain,CrRbcX-IIa
B: Ribulose bisphosphate carboxylase large chain,CrRbcX-IIa
R: Ribulose bisphosphate carboxylase large chain


Theoretical massNumber of molelcules
Total (without water)30,6883
Polymers30,6883
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-37 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.217, 38.525, 50.355
Angle α, β, γ (deg.)88.470, 81.530, 67.920
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 44 - 156 / Label seq-ID: 20 - 132

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ribulose bisphosphate carboxylase large chain,CrRbcX-IIa / RuBisCO large subunit


Mass: 14917.970 Da / Num. of mol.: 2 / Fragment: UNP residues 462-473,UNP residues 44-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: rbcL, CGL41, CHLREDRAFT_162607 / Plasmid: pHue / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00877, UniProt: A8HQH2, ribulose-bisphosphate carboxylase
#2: Protein/peptide Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 852.030 Da / Num. of mol.: 1 / Fragment: UNP residues 462-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: rbcL / Plasmid: pHue / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00877, ribulose-bisphosphate carboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl pH 8.5, 25% PEG2000 MME / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.97→49.781 Å / Num. all: 15820 / Num. obs: 15820 / % possible obs: 94.2 % / Redundancy: 2.4 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.102 / Rsym value: 0.081 / Net I/av σ(I): 6.511 / Net I/σ(I): 10.4 / Num. measured all: 38750
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.97-2.072.20.4941.6481821520.3940.494287.9
2.07-2.22.50.3032.2541821930.230.3033.994.8
2.2-2.352.40.2252.7509020880.1680.2255.495.9
2.35-2.542.30.163.7453119440.1190.167.495.2
2.54-2.782.60.134.2471118170.0910.1310.197.1
2.78-3.112.50.0985.6419216540.070.09812.997.4
3.11-3.592.50.0629.1360014220.0440.06217.995.8
3.59-4.42.60.04313.7299311680.030.04323.593.4
4.4-6.222.40.03914.721698940.0290.03923.792.7
6.22-35.6832.50.03412.812284880.0280.03426.591

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BS1

5bs1


Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2156 / WRfactor Rwork: 0.197 / FOM work R set: 0.8017 / SU B: 11.071 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2048 / SU Rfree: 0.1606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 810 5.1 %RANDOM
Rwork0.1996 ---
obs0.2007 15009 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.7 Å2 / Biso mean: 30.375 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20.57 Å22.89 Å2
2--4.42 Å2-1.71 Å2
3----3.84 Å2
Refinement stepCycle: final / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 87 1887
Biso mean---36.99 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191832
X-RAY DIFFRACTIONr_bond_other_d0.0050.021740
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9612471
X-RAY DIFFRACTIONr_angle_other_deg1.09233975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.93723.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44415314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0631518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022090
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02428
Refine LS restraints NCS

Ens-ID: 1 / Number: 5742 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.966→2.017 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 66 -
Rwork0.382 1022 -
all-1088 -
obs--84.6 %
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)
10.6145-0.964-1.66331.88752.9226.73180.0056-0.05210.0746-0.1170.1778-0.0984-0.17250.2534-0.18340.0509-0.038-0.06660.0340.02910.22656.2187-3.9168-7.9377
20.7516-1.2293-1.05143.50522.87983.2952-0.04840.0502-0.02990.0351-0.03570.09630.0209-0.23990.08410.0291-0.0144-0.06720.0570.03320.1902-6.62356.04566.9631
318.3691-14.3247-7.23211.22035.63762.88690.05521.0665-1.09390.0897-0.66440.81890.0042-0.35520.60920.33210.156-0.08430.41510.07340.4353-14.040415.02611.5303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 156
2X-RAY DIFFRACTION1D1 - 27
3X-RAY DIFFRACTION2B44 - 156
4X-RAY DIFFRACTION2E1 - 39
5X-RAY DIFFRACTION3R462 - 467

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