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- PDB-4mkv: Structure of Pisum sativum Rubisco with ABA -

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Basic information

Entry
Database: PDB / ID: 4mkv
TitleStructure of Pisum sativum Rubisco with ABA
Components(Ribulose bisphosphate carboxylase ...RuBisCO) x 2
KeywordsLYASE / rubisco / ribulose-1 / 5-bisphosphate / garden pea / abscisic acid
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain ...Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / 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
Chem-A8S / PHOSPHATE ION / RIBULOSE-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 3
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLoewen, M.C. / Loewen, P.C. / Switala, J.
CitationJournal: Plos One / Year: 2015
Title: Identification of Interactions between Abscisic Acid and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase.
Authors: Galka, M.M. / Rajagopalan, N. / Buhrow, L.M. / Nelson, K.M. / Switala, J. / Cutler, A.J. / Palmer, D.R. / Loewen, P.C. / Abrams, S.R. / Loewen, M.C.
History
DepositionSep 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
T: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
U: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
V: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,02516
Polymers262,2358
Non-polymers1,7908
Water18,5551030
1
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
T: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
U: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
V: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
hetero molecules

A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
S: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
T: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
U: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
V: Ribulose bisphosphate carboxylase small chain 3A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,05032
Polymers524,47116
Non-polymers3,57916
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area104660 Å2
ΔGint-427 kcal/mol
Surface area119500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.440, 110.230, 203.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
DetailsThe biological assembly is a hexadecamer generated from the octamer in the asymmetric unit by the operation -X, Y, -Z plus translation 0, -1, 0.

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Components

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Ribulose bisphosphate carboxylase ... , 2 types, 8 molecules ABCDSTUV

#1: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit / Ribulose-1 / 5-bisphosphate carboxylase oxygenase


Mass: 50999.855 Da / Num. of mol.: 4 / Fragment: UNP residues 12-469 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Tissue: leaf
References: UniProt: P04717, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small chain 3A, chloroplastic / RuBisCO small subunit 3A


Mass: 14558.974 Da / Num. of mol.: 4 / Fragment: UNP residues 58-180 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Tissue: leaf
References: UniProt: P07689, ribulose-bisphosphate carboxylase

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Sugars , 1 types, 4 molecules

#3: Sugar
ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE / Ribulose 1,5-bisphosphate


Type: saccharideCarbohydrate / Mass: 310.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2

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Non-polymers , 3 types, 1034 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid, (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid / Abscisic acid


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4 / Comment: hormone*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1030 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG6000, 0.1 M HEPES, pH 7.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2011 / Details: mirrors
RadiationMonochromator: Double crystal SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→110.23 Å / Num. all: 128333 / Num. obs: 128333 / % possible obs: 95.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 27.95 Å2 / Rsym value: 0.114 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.272.70.4461.551625190350.44697.4
2.27-2.42.80.3372.149338179230.33797.1
2.4-2.572.80.2592.846464167870.25996.7
2.57-2.782.80.1853.943379155560.18596.3
2.78-3.042.80.1345.440049142860.13495.8
3.04-3.42.80.1165.736316128820.11695.3
3.4-3.932.90.0867.632224113010.08694.4
3.93-4.812.90.06210.62719294170.06293.2
4.81-6.82.90.05411.22108772110.05491.5
6.8-48.5152.90.03616.21147439350.03688.5

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.51 Å / Cor.coef. Fo:Fc: 0.9462 / Cor.coef. Fo:Fc free: 0.9247 / Occupancy max: 1 / Occupancy min: 0.3 / SU R Cruickshank DPI: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 6458 5.03 %RANDOM
Rwork0.1621 ---
obs0.1639 128282 94.93 %-
Displacement parametersBiso max: 131.24 Å2 / Biso mean: 30.2652 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-6.0915 Å20 Å20 Å2
2---3.1835 Å20 Å2
3----2.908 Å2
Refine analyzeLuzzati coordinate error obs: 0.213 Å
Refinement stepCycle: LAST / Resolution: 2.15→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18488 0 106 1030 19624
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6595SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes412HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2850HARMONIC5
X-RAY DIFFRACTIONt_it19210HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2381SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23379SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19210HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg26083HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion17.81
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2416 490 5.06 %
Rwork0.2022 9190 -
all0.2042 9680 -
obs--94.93 %

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