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- PDB-2pen: Crystal structure of RbcX, crystal form I -

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Basic information

Entry
Database: PDB / ID: 2pen
TitleCrystal structure of RbcX, crystal form I
ComponentsORF134
KeywordsCHAPERONE / helix bundle / protein complex assembly
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / carboxysome / carbon fixation / protein folding chaperone / photosynthesis / protein homodimerization activity / cytoplasm
Similarity search - Function
RuBisCO chaperone RbcX / 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
RuBisCO chaperone RbcX
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsSaschenbrecker, S. / Bracher, A. / Vasudeva Rao, K. / Vasudeva Rao, B. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structure and Function of RbcX, an Assembly Chaperone for Hexadecameric Rubisco.
Authors: Saschenbrecker, S. / Bracher, A. / Rao, K.V. / Rao, B.V. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionApr 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF134
B: ORF134
C: ORF134
D: ORF134
E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)91,7056
Polymers91,7056
Non-polymers00
Water34219
1
A: ORF134
B: ORF134


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-39 kcal/mol
Surface area11470 Å2
MethodPISA
2
C: ORF134
D: ORF134


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-33 kcal/mol
Surface area11470 Å2
MethodPISA
3
E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-39 kcal/mol
Surface area11630 Å2
MethodPISA
4
C: ORF134
D: ORF134

E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)61,1364
Polymers61,1364
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z+1/41
Buried area10750 Å2
ΔGint-81 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.335, 93.335, 411.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe biological unit is a dimer. There are 3 biological units in the asymmetric unit (chains A & B, chains C & D and chains E & F).

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Components

#1: Protein
ORF134


Mass: 15284.084 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7002 / Gene: RbcX / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q44177
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.89 Å3/Da / Density % sol: 74.85 %
Description: Data collected at ESRF BEAMLINE BM14 using wavelength 0.8793 A was for Pt derivative
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.30-1.55 M Sodium acetate, 0.1 M HEPES-NaOH pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9789
SYNCHROTRONESRF BM1420.8793
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJun 18, 2005
MARMOSAIC 225 mm CCD2CCDJun 30, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.87931
Reflection
Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsRsym valueD res high (Å)D res low (Å)Num. obs% possible obs
714.32290450.0810.0813.15102.06232533100
7.4263378950.0780.0782.8102.5984574599.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
9.9693.2599.410.0360.0365.7
7.049.9699.910.0360.0366.6
5.757.0410010.0610.0616.9
4.985.7510010.0670.0677
4.454.9810010.0610.0617.1
4.074.4510010.0740.0747.1
3.764.0710010.1250.1257.2
3.523.7610010.1940.1947.2
3.323.5210010.3340.3347.2
3.153.3210010.6210.6217.2
8.8593.6699.520.0290.0296.1
6.268.8599.620.0390.0397
5.116.2699.520.0540.0547.2
4.435.1199.320.0470.0477.3
3.964.4399.320.0560.0567.4
3.613.9699.120.0880.0887.5
3.353.6199.120.1470.1477.5
3.133.3598.920.2990.2997.5
2.953.1398.920.5460.5467.6
2.82.9598.720.8640.8647.6
ReflectionResolution: 2.8→411.99 Å / Num. obs: 46362 / % possible obs: 100 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.9514.80.6411.29824166170.641100
2.95-3.1314.80.4231.89323162850.423100
3.13-3.3514.80.2393.18768659260.239100
3.35-3.6114.80.1275.78129155080.127100
3.61-3.9614.70.0838.27501251060.083100
3.96-4.4314.60.05910.76845546880.059100
4.43-5.1114.40.0619.15982841430.061100
5.11-6.2614.20.0817.15084735730.081100
6.26-8.8513.80.05310.13908128220.053100
8.85-91.0312.10.03614.82052216940.03699.2

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.4 / FOM acentric: 0.43 / FOM centric: 0.36 / Reflection: 1067 / Reflection acentric: 641 / Reflection centric: 426
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-24.8340.40.430.361067641426
5-8
4-5
3.5-4
3-3.5
2.8-3
Phasing MIR der
IDDer set-ID
11
21
31
41
51
61
Phasing MIR der site

ID: 1 / Biso : 60 Å / Atom type symbol: Pt

Der-IDFract xFract yFract zOccupancy
10.73260.99210.09550.357
20.05970.08970.12140.3104
30.20270.18640.08120.37
40.52210.07340.07010.3047
50.05210.55360.00450.2283
60.24550.44670.03120.2888

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVE2.01phasing
RESOLVE2.01phasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.742 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2321 5 %RANDOM
Rwork0.24 ---
obs0.242 46068 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 0 19 5105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225158
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9786994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80824.336226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.64615908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8451537
X-RAY DIFFRACTIONr_chiral_restr0.0930.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023803
X-RAY DIFFRACTIONr_nbd_refined0.2440.22483
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23589
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0190.21
X-RAY DIFFRACTIONr_mcbond_it0.6941.53352
X-RAY DIFFRACTIONr_mcangle_it1.27925219
X-RAY DIFFRACTIONr_scbond_it1.78831997
X-RAY DIFFRACTIONr_scangle_it3.0814.51775
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 167 -
Rwork0.354 3123 -
obs-3290 100 %

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