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- PDB-5bs1: Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 5bs1
TitleCrystal structure of RbcX-IIa from Chlamydomonas reinhardtii
ComponentsCrRbcX-IIa
KeywordsCHAPERONE / RbcX
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / carbon fixation / photosynthesis / protein folding chaperone
Similarity search - Function
Chaperonin-like RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsBracher, A. / Hauser, T. / Liu, C. / Hartl, F.U. / Mayer-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 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _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: CrRbcX-IIa
B: CrRbcX-IIa
C: CrRbcX-IIa
D: CrRbcX-IIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8835
Polymers56,8594
Non-polymers241
Water6,990388
1
A: CrRbcX-IIa
B: CrRbcX-IIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4543
Polymers28,4292
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-39 kcal/mol
Surface area13180 Å2
MethodPISA
2
C: CrRbcX-IIa
D: CrRbcX-IIa


Theoretical massNumber of molelcules
Total (without water)28,4292
Polymers28,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-43 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.133, 52.989, 61.561
Angle α, β, γ (deg.)76.490, 81.100, 70.100
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEAA34 - 1561 - 123
21MSEMSEBB34 - 1561 - 123
12ALAALAAA34 - 1531 - 120
22ALAALACC34 - 1531 - 120
13ALAALAAA34 - 1541 - 121
23ALAALADD34 - 1541 - 121
14ALAALABB34 - 1531 - 120
24ALAALACC34 - 1531 - 120
15ALAALABB34 - 1541 - 121
25ALAALADD34 - 1541 - 121
16ALAALACC34 - 1541 - 121
26ALAALADD34 - 1541 - 121

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
CrRbcX-IIa


Mass: 14214.679 Da / Num. of mol.: 4 / Fragment: UNP residues 35-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CGL41, CHLREDRAFT_162607 / Plasmid: pHue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8HQH2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 5 % PEG-3350, 0.2 M MgCl2, 50 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 2.4 % / Number: 137620 / Rsym value: 0.049 / D res high: 1.498 Å / D res low: 48.87 Å / Num. obs: 56366 / % possible obs: 84.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
4.7348.8710.0330.0332.5
3.344.7310.0330.0332.4
2.733.3410.0380.0382.5
2.362.7310.0450.0452.6
2.112.3610.0560.0562.4
1.932.1110.0750.0752.6
1.791.9310.1170.1172.4
1.671.7910.1760.1762.5
1.581.6710.2330.2332.4
1.4991.5810.3080.3082
ReflectionResolution: 1.498→48.87 Å / Num. all: 56366 / Num. obs: 56366 / % possible obs: 84.2 % / Redundancy: 2.4 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.087 / Rsym value: 0.049 / Net I/av σ(I): 9.455 / Net I/σ(I): 10.7 / Num. measured all: 137620
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
1.498-1.5820.3082.4713934990.2730.3082.436.8
1.58-1.672.40.2333.21497263160.2080.2333.468.1
1.67-1.792.50.1764.22083483290.1540.1764.595.1
1.79-1.932.40.1176.11887377870.1070.1176.495.7
1.93-2.112.60.0759.21856072370.0730.0759.796.3
2.11-2.362.40.05612.41592765230.060.05612.896.9
2.36-2.732.60.04514.81487758250.050.0451697.6
2.73-3.342.50.03816.21212549390.0450.03819.398
3.34-4.732.40.03317.8917638190.0370.0332498.3
4.73-48.872.50.03317513720920.0450.03324.298.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
SHELXphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2142 / WRfactor Rwork: 0.1831 / FOM work R set: 0.8778 / SU B: 1.719 / SU ML: 0.061 / SU R Cruickshank DPI: 0.1058 / SU Rfree: 0.0999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2585 5 %RANDOM
Rwork0.1772 ---
obs0.1787 49112 94.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.4 Å2 / Biso mean: 18.804 Å2 / Biso min: 6.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.37 Å2-0.04 Å2
2---0.13 Å20.04 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 1 388 4047
Biso mean--32.9 29.4 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193871
X-RAY DIFFRACTIONr_bond_other_d0.0070.023687
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9895224
X-RAY DIFFRACTIONr_angle_other_deg1.41338426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9265492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.2122.473186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94815565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2341547
X-RAY DIFFRACTIONr_chiral_restr0.0750.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024475
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02940
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A57090.18
12B57090.18
21A63140.12
22C63140.12
31A55510.18
32D55510.18
41B54410.18
42C54410.18
51B57480.13
52D57480.13
61C54390.18
62D54390.18
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 137 -
Rwork0.229 2589 -
all-2726 -
obs--66.6 %

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