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- PDB-3q20: Crystal structure of RbcX C103A mutant from Thermosynechococcus e... -

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Basic information

Entry
Database: PDB / ID: 3q20
TitleCrystal structure of RbcX C103A mutant from Thermosynechococcus elongatus
ComponentsRbcX protein
KeywordsCHAPERONE / helix bundle / RuBisCO assembly
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / carboxysome / carbon fixation / photosynthesis / protein folding chaperone / cytoplasm
Similarity search - Function
Chaperonin-like RbcX / RuBisCO chaperone 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
ACETATE ION / HEXANE-1,6-DIOL / RuBisCO chaperone RbcX
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsTarnawski, M. / Krzywda, S. / Szczepaniak, A. / Jaskolski, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of the RuBisCO chaperone RbcX from the thermophilic cyanobacterium Thermosynechococcus elongatus
Authors: Tarnawski, M. / Krzywda, S. / Bialek, W. / Jaskolski, M. / Szczepaniak, A.
History
DepositionDec 19, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 26, 2011ID: 3KA1
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: RbcX protein
B: RbcX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4996
Polymers29,1452
Non-polymers3544
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-34 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.780, 67.733, 94.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RbcX protein


Mass: 14572.369 Da / Num. of mol.: 2 / Mutation: C103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: rbcX, tll1505 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DIS6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate, 1.0M 1,6-hexanediol, 0.01M cobalt(II) chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 2, 2008
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→41.2 Å / Num. obs: 31245 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 29.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / % possible all: 71.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PEQ

2peq


Resolution: 1.71→41.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.771 / SU ML: 0.07 / Cross valid method: R FREE / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21112 1280 4.1 %RANDOM
Rwork0.18203 ---
obs0.1833 29886 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.773 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2---0.46 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 24 208 2029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221861
X-RAY DIFFRACTIONr_bond_other_d0.0010.021283
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9682508
X-RAY DIFFRACTIONr_angle_other_deg2.23333123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.135220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92724.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25515344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4741518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
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_it0.9081.51103
X-RAY DIFFRACTIONr_mcbond_other0.2961.5439
X-RAY DIFFRACTIONr_mcangle_it1.51721785
X-RAY DIFFRACTIONr_scbond_it2.2893758
X-RAY DIFFRACTIONr_scangle_it3.7544.5722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 49 -
Rwork0.264 1457 -
obs--63.44 %
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)
116.87494.26450.26783.46450.42892.01210.0509-0.10130.4488-0.19450.10.3283-0.41170.0327-0.1510.1882-0.0540.04480.1216-0.03670.136410.220.693217.6936
25.37192.35222.71013.06070.14216.1638-0.2772-0.03790.8597-0.01890.1730.3952-1.44830.54650.10420.5011-0.33970.10660.3392-0.13290.192230.563310.428414.2417
33.68211.296-2.26611.39070.92626.09520.05850.1270.0431-0.30910.2209-0.038-0.91340.6979-0.27940.2877-0.21480.0820.3216-0.09810.205925.04931.804210.6144
45.3484-4.3626-5.629110.80988.841310.5502-0.3411-0.1217-0.2030.57590.1789-0.09150.52990.32450.16220.13490.0034-0.01580.1460.0590.161711.912-4.438732.4933
54.3409-3.0062-0.334112.73922.320812.469-0.1656-0.30690.180.96230.1701-0.1108-0.51660.3409-0.00460.2202-0.0469-0.0310.12480.01030.05654.33978.561943.1998
616.6751-22.1049-7.831429.326410.37293.6853-1.4902-1.2825-0.57081.80251.3770.76960.56510.69210.11321.4952-0.210.22811.7662-0.2030.33240.103117.360150.2188
79.274-2.8069-2.21816.44281.16126.1737-0.1122-0.32810.11140.18220.2746-0.80670.18790.8965-0.16230.21430.0269-0.0210.3651-0.02750.351620.65661.522728.5152
82.2751-2.02920.29163.481-1.23142.29230.23240.20570.0234-0.25-0.12340.1754-0.0449-0.151-0.1090.284-0.004-0.00480.2319-0.00120.2973-2.988111.800225.5655
93.1698-1.6592-0.08443.8137-0.23312.0774-0.017-0.03170.13430.11860.0292-0.0515-0.16450.0602-0.01210.2897-0.02340.00040.24380.00620.27971.60589.45732.8023
103.84290.8601-4.34231.2584-1.56366.58630.04780.105-0.0593-0.1263-0.0508-0.0598-0.18090.25050.0030.232-0.0640.01260.2269-0.04930.212516.2602-5.376110.2854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2A22 - 52
3X-RAY DIFFRACTION3A53 - 83
4X-RAY DIFFRACTION4A84 - 97
5X-RAY DIFFRACTION5A98 - 107
6X-RAY DIFFRACTION6A108 - 114
7X-RAY DIFFRACTION7B2 - 13
8X-RAY DIFFRACTION8B14 - 48
9X-RAY DIFFRACTION9B49 - 81
10X-RAY DIFFRACTION10B82 - 107

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