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- PDB-2qyg: Crystal Structure of a RuBisCO-like Protein rlp2 from Rhodopseudo... -

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Basic information

Entry
Database: PDB / ID: 2qyg
TitleCrystal Structure of a RuBisCO-like Protein rlp2 from Rhodopseudomonas palustris
ComponentsRibulose bisphosphate carboxylase-like protein 2
KeywordsUNKNOWN FUNCTION / beta-alpha-barrel
Function / homology
Function and homology information


carbon fixation / ribulose-bisphosphate carboxylase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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 / Alpha-Beta Plaits ...Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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 / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase-like protein 2
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLi, H. / Chan, S. / Tabita, F.R. / Eisenberg, D.
CitationJournal: Microbiol.Mol.Biol.Rev. / Year: 2007
Title: Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs.
Authors: Tabita, F.R. / Hanson, T.E. / Li, H. / Satagopan, S. / Singh, J. / Chan, S.
History
DepositionAug 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
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.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase-like protein 2
B: Ribulose bisphosphate carboxylase-like protein 2
C: Ribulose bisphosphate carboxylase-like protein 2
D: Ribulose bisphosphate carboxylase-like protein 2


Theoretical massNumber of molelcules
Total (without water)194,7544
Polymers194,7544
Non-polymers00
Water00
1
A: Ribulose bisphosphate carboxylase-like protein 2
B: Ribulose bisphosphate carboxylase-like protein 2


Theoretical massNumber of molelcules
Total (without water)97,3772
Polymers97,3772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
MethodPISA
2
C: Ribulose bisphosphate carboxylase-like protein 2
D: Ribulose bisphosphate carboxylase-like protein 2


Theoretical massNumber of molelcules
Total (without water)97,3772
Polymers97,3772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.662, 119.529, 203.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 1 - 429 / Label seq-ID: 21 - 449

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Ribulose bisphosphate carboxylase-like protein 2 / RuBisCO-like protein


Mass: 48688.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: rlp2 / Plasmid: BL21-Gold(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ND47

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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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 280mM ammonium acetate, 100mM sodium acetate, 30% PEG4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→90 Å / Num. all: 26399 / Num. obs: 26399 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.164 / Net I/σ(I): 9.6
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2572 / Rsym value: 0.467 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YKW

1ykw


Resolution: 3.3→77.38 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.868 / SU B: 56.672 / SU ML: 0.413 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.568 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23228 1307 5.1 %RANDOM
Rwork0.2025 ---
all0.20402 24549 --
obs0.20402 24549 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.223 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--0.17 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 3.3→77.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13012 0 0 0 13012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213380
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.96518224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94451712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04822.517588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.041151960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8915120
X-RAY DIFFRACTIONr_chiral_restr0.0930.21964
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210568
X-RAY DIFFRACTIONr_nbd_refined0.2280.25939
X-RAY DIFFRACTIONr_nbtor_refined0.3170.29154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3860.2108
X-RAY DIFFRACTIONr_mcbond_it0.6011.58686
X-RAY DIFFRACTIONr_mcangle_it1.102213740
X-RAY DIFFRACTIONr_scbond_it1.3135102
X-RAY DIFFRACTIONr_scangle_it2.3854.54484
Refine LS restraints NCS

Ens-ID: 1 / Number: 3254 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
3Ctight positional0.050.05
4Dtight positional0.050.05
1Atight thermal0.060.5
2Btight thermal0.060.5
3Ctight thermal0.060.5
4Dtight thermal0.060.5
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 103 -
Rwork0.268 1754 -
obs-1754 99.46 %
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)
10.65810.5729-0.36051.3075-0.73270.6802-0.0152-0.09540.00330.04980.02980.0263-0.01080.1237-0.0145-0.1326-0.00130.0138-0.07980.0213-0.149320.286-11.1746-11.1839
23.34170.82470.50331.25350.05241.06280.021-0.0020.25360.0809-0.05070.1736-0.10730.09910.0297-0.00450.00750.0813-0.0615-0.0158-0.097523.14367.70755.4712
32.3978-1.0990.00321.58740.18210.61990.05240.01710.1714-0.0249-0.02330.0845-0.0918-0.1271-0.0291-0.1032-0.0246-0.0087-0.144-0.0037-0.160415.6433-17.5327-59.9262
41.1604-0.73030.35212.7319-0.41360.94760.00880.03580.0715-0.13210.01940.00080.122-0.0218-0.0282-0.1631-0.02040.0041-0.1235-0.0004-0.198417.94541.3123-43.2774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 42921 - 449
2X-RAY DIFFRACTION2BB1 - 42921 - 449
3X-RAY DIFFRACTION3CC1 - 42921 - 449
4X-RAY DIFFRACTION4DD1 - 42921 - 449

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