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- PDB-5hqm: Structure function studies of R. palustris RubisCO (R. palustris/... -

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Basic information

Entry
Database: PDB / ID: 5hqm
TitleStructure function studies of R. palustris RubisCO (R. palustris/R. rubrum chimera)
ComponentsRibulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
KeywordsLYASE / RubisCO / hexamer
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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 ...Ribulose bisphosphate carboxylase large subunit, type II / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / : / Ribulose bisphosphate carboxylase / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
Rhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsArbing, M.A. / Shin, A. / Cascio, D. / Satagopan, S. / Tabita, F.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095742 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: To Be Published
Title: Structure function studies of R. palustris RubisCO.
Authors: Arbing, M.A. / Satagopan, S. / Varaljay, V.A. / Tabita, F.R.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5578
Polymers106,7182
Non-polymers8396
Water7,530418
1
A: Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
hetero molecules

A: Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
hetero molecules

A: Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,67124
Polymers320,1546
Non-polymers2,51718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)165.120, 165.120, 95.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase / RuBisCO


Mass: 53358.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic), (gene. exp.) Rhodospirillum rubrum (bacteria)
Plasmid: pET28a / Gene: cbbM, cbbL2, rbpL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6N0W9, UniProt: P04718, ribulose-bisphosphate carboxylase
#2: Sugar ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O13P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Reservoir solution: 0.4 M Sodium phosphate monobasic/1.6 M Potassium phosphate dibasic, 0.1 M Imidazole (pH 8.0), 0.2 M NaCl. Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% ...Details: Reservoir solution: 0.4 M Sodium phosphate monobasic/1.6 M Potassium phosphate dibasic, 0.1 M Imidazole (pH 8.0), 0.2 M NaCl. Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% Glycerol, 10 mM MgCl2, 20 mM NaHCO3.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→82.56 Å / Num. obs: 76203 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 33.61 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.059 / Χ2: 1.034 / Net I/σ(I): 17.19 / Num. measured all: 386908
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.955.10.8690.6112.3427709563155000.68297.7
1.95-20.9270.4333.3928296553155250.48399.9
2-2.060.9490.3574.0725792536053530.40199.9
2.06-2.120.9690.285.3227359524152380.31299.9
2.12-2.190.9760.2376.3526958503150280.26399.9
2.19-2.270.9850.1828.0225889490448990.20399.9
2.27-2.350.9890.1499.8324519469246900.166100
2.35-2.450.9920.12311.7622970456245550.13799.8
2.45-2.560.9940.10313.4420902431443030.11699.7
2.56-2.680.9960.0916.0422468418841880.099100
2.68-2.830.9970.07219.720685393039220.0899.8
2.83-30.9980.05723.8519258376337470.06499.6
3-3.210.9980.04628.4916635349234690.05199.3
3.21-3.470.9990.03734.8716225331132920.04299.4
3.47-3.80.9990.03340.1815004297629730.03799.9
3.8-4.240.9990.03143.5313365273327260.03499.7
4.24-4.90.9990.02843.8810528238323420.03298.3
4.9-60.9990.02846.110420204820450.03299.9
6-8.490.9990.02647.057596155615490.02999.6
8.49-82.560.9990.02351.5543308638590.02699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
BUSTER-TNT2.10.0refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LF1

4lf1


Resolution: 1.95→82.56 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 7040 10 %RANDOM
Rwork0.1672 ---
obs0.1697 70396 99.74 %-
Displacement parametersBiso max: 152.37 Å2 / Biso mean: 45.15 Å2 / Biso min: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1-8.528 Å20 Å20 Å2
2--8.528 Å20 Å2
3----17.056 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.95→82.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6945 0 64 418 7427
Biso mean--47.58 44.57 -
Num. residues----913
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3796SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes164HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2119HARMONIC5
X-RAY DIFFRACTIONt_it13694HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion922SEMIHARMONIC5
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_contact15525SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13706HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg24574HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion4.1
X-RAY DIFFRACTIONt_other_torsion2.88
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2238 520 9.99 %
Rwork0.1931 4683 -
all0.1961 5203 -
obs--99.74 %
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)
10.97660.02710.17020.91460.13480.2870.0007-0.12610.34820.07650.0498-0.2716-0.07560.045-0.0505-0.1075-0.01950.0173-0.1247-0.08570.02415.151327.698229.9579
21.00980.04310.13860.96770.27570.4507-0.0040.03630.1008-0.06520.0686-0.4319-0.06430.1484-0.0645-0.1346-0.01790.0143-0.1062-0.03890.045530.27166.945120.2168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 461
2X-RAY DIFFRACTION2{ B|* }B1 - 454

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