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- PDB-2pei: Crystal structure of selenomethionine-labeled RbcX -

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Basic information

Entry
Database: PDB / ID: 2pei
TitleCrystal structure of selenomethionine-labeled RbcX
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 / SAD / Resolution: 2.7 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

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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
G: ORF134
H: ORF134
I: ORF134
J: ORF134
K: ORF134
L: ORF134


Theoretical massNumber of molelcules
Total (without water)154,16612
Polymers154,16612
Non-polymers00
Water75742
1
A: ORF134
B: ORF134


Theoretical massNumber of molelcules
Total (without water)25,6942
Polymers25,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-37 kcal/mol
Surface area11220 Å2
MethodPISA
2
C: ORF134
D: ORF134


Theoretical massNumber of molelcules
Total (without water)25,6942
Polymers25,6942
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-35 kcal/mol
Surface area11270 Å2
MethodPISA
3
E: ORF134
F: ORF134


Theoretical massNumber of molelcules
Total (without water)25,6942
Polymers25,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-37 kcal/mol
Surface area11440 Å2
MethodPISA
4
G: ORF134
H: ORF134


Theoretical massNumber of molelcules
Total (without water)25,6942
Polymers25,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-33 kcal/mol
Surface area11490 Å2
MethodPISA
5
I: ORF134
J: ORF134


Theoretical massNumber of molelcules
Total (without water)25,6942
Polymers25,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-36 kcal/mol
Surface area11130 Å2
MethodPISA
6
K: ORF134
L: ORF134


Theoretical massNumber of molelcules
Total (without water)25,6942
Polymers25,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-38 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.362, 71.102, 113.162
Angle α, β, γ (deg.)89.580, 81.100, 80.090
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a dimer. There are 6 biological units in the asymmetric unit (chains A & B,C & D, E & F, G & H, I & J and K & L).

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Components

#1: Protein
ORF134


Mass: 12847.202 Da / Num. of mol.: 12 / Fragment: core domain, residues 1-109
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 / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.57 Å3/Da / Density % sol: 65.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.1 M Tris-HCl pH 8.5, 0.2 M Sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→111.803 Å / Num. obs: 56794 / % possible obs: 96.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.853.80.421.53183882800.4296.3
2.85-3.023.90.3012.23011477930.30196.4
3.02-3.233.90.2053.32858873760.20596.7
3.23-3.493.90.1325.22655868310.13296.8
3.49-3.823.90.0926.92460163300.09297
3.82-4.273.90.0729.42223857100.07297.1
4.27-4.933.90.06310.41967850820.06397.3
4.93-6.043.90.0718.61652842780.07197.5
6.04-8.543.80.05611.61263632990.05697.5
8.54-68.523.70.04312.9664018150.04397.4

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-17.24814.346-0.113SE51.510.74
22.98-5.89814.01SE56.580.79
315.561-9.904-9.112SE76.870.53
46.35510.8176.785SE65.410.35
551.38152.461-1.31SE50.271.11
641.17145.38222.773SE47.990.49
737.31320.69814.691SE57.51.06
857.23238.18220.053SE59.070.53
945.7644.43763.541SE51.130.61
1058.41714.46485.509SE56.520.64
1155.909-8.26598.519SE52.50.73
1268.1932.48976.63SE56.820.6
130.931-0.22233.603SE46.770.8
1422.02816.62530.576SE54.80.66
1534.6017.22751.524SE45.20.84
1626.043-0.50426.519SE69.610.66
1768.40615.54150.159SE49.770.75
1851.99539.20837.324SE55.060.69
1950.19552.72560.265SE58.670.55
2070.40136.89791.349SE58.130.38
21-18.1694.911.119SE54.140.24
2260.60551.812-1.222SE78.470.59
2352.0741.62757.476SE60.450.41
2453.858-1.388104.95SE58.050.58
251.896-7.69528.267SE72.920.58
2635.51416.49251.619SE57.720.38
2759.18216.22349.59SE65.510.31
2892.36910.80771.017SE77.770.5
2988.84237.75672.701SE73.830.38
3067.53743.02685.059SE48.380.63
3128.7997.81778.161SE48.510.33
3269.46666.008104.898SE66.750.34
3342.61854.85255.389SE66.150.58
3451.69226.75128.553SE57.010.43
3511.4711.3016.865SE71.640.33
368.66313.55625.34SE56.130.43
3746.14950.335107.87SE42.160.22
Phasing dmFOM : 0.57 / FOM acentric: 0.57 / FOM centric: 0 / Reflection: 56792 / Reflection acentric: 56792 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
7.7-111.8030.910.9124412441
4.8-7.70.80.876027602
3.9-4.80.810.8195509550
3.4-3.90.670.6795869586
2.9-3.40.420.421704317043
2.7-2.90.240.241057010570

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHARPphasing
RESOLVE2.01phasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.925 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.509 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2881 5.1 %RANDOM
Rwork0.212 ---
obs0.215 56651 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.164 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å21.85 Å20.32 Å2
2---0.72 Å20.19 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10026 0 0 42 10068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02110167
X-RAY DIFFRACTIONr_bond_other_d0.0020.029594
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.97313755
X-RAY DIFFRACTIONr_angle_other_deg0.919322167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62451268
X-RAY DIFFRACTIONr_chiral_restr0.0840.21637
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211133
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021944
X-RAY DIFFRACTIONr_nbd_refined0.2420.22596
X-RAY DIFFRACTIONr_nbd_other0.2310.210906
X-RAY DIFFRACTIONr_nbtor_other0.0930.26615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.24
X-RAY DIFFRACTIONr_mcbond_it0.7351.56376
X-RAY DIFFRACTIONr_mcangle_it1.49210204
X-RAY DIFFRACTIONr_scbond_it2.58433791
X-RAY DIFFRACTIONr_scangle_it4.4534.53551
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.366 215
Rwork0.286 3875
obs-4090

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