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- PDB-5hk4: Structure function studies of R. palustris RubisCO (A47V-M331A mutant) -

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Basic information

Entry
Database: PDB / ID: 5hk4
TitleStructure function studies of R. palustris RubisCO (A47V-M331A mutant)
ComponentsRibulose 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
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsArbing, M.A. / Shin, A. / Cascio, D. / Satagopan, S. / North, J.A. / 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 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 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
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
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
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
E: Ribulose bisphosphate carboxylase
F: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,63418
Polymers316,3526
Non-polymers2,28312
Water17,312961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.090, 100.410, 100.320
Angle α, β, γ (deg.)113.06, 88.86, 108.01
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B
311CHAIN C
411CHAIN D
511CHAIN E
611CHAIN F

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Components

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO


Mass: 52725.277 Da / Num. of mol.: 6 / Mutation: A47V,M331A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6N0W9, ribulose-bisphosphate carboxylase
#2: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O13P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% Glycerol, 10 mM MgCl2, 20 mM NaHCO3. Protein concentration: 16 mg/ml. Reservoir solution: 20-24% PEG 3350, 200 mM sodium sulfate, ...Details: Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% Glycerol, 10 mM MgCl2, 20 mM NaHCO3. Protein concentration: 16 mg/ml. Reservoir solution: 20-24% PEG 3350, 200 mM sodium sulfate, 100 mM Bis-Tris Propane pH 7-8.
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.15→81.96 Å / Num. obs: 133906 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 35.34 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.88
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 1.9 / % possible all: 87.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LF1

4lf1


Resolution: 2.15→81.96 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.255 13378 10 %Random selection
Rwork0.225 ---
obs0.228 133810 95.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.51 Å2
Refinement stepCycle: LAST / Resolution: 2.15→81.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21115 0 132 961 22208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421823
X-RAY DIFFRACTIONf_angle_d0.75629511
X-RAY DIFFRACTIONf_dihedral_angle_d10.8187823
X-RAY DIFFRACTIONf_chiral_restr0.0313071
X-RAY DIFFRACTIONf_plane_restr0.0043909
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A16320X-RAY DIFFRACTIONPOSITIONAL
12B16320X-RAY DIFFRACTIONPOSITIONAL
13C16320X-RAY DIFFRACTIONPOSITIONAL
14D16320X-RAY DIFFRACTIONPOSITIONAL
15E16320X-RAY DIFFRACTIONPOSITIONAL
16F16320X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1499-2.17440.31624140.27423727X-RAY DIFFRACTION87
2.1744-2.20.31834000.28473598X-RAY DIFFRACTION87
2.2-2.22680.61364250.57873835X-RAY DIFFRACTION90
2.2268-2.2550.4714160.45443736X-RAY DIFFRACTION90
2.255-2.28470.41264290.3683864X-RAY DIFFRACTION91
2.2847-2.3160.30744330.27133902X-RAY DIFFRACTION92
2.316-2.3490.28124360.23923920X-RAY DIFFRACTION94
2.349-2.38410.26384390.2373953X-RAY DIFFRACTION93
2.3841-2.42140.28174290.23163855X-RAY DIFFRACTION93
2.4214-2.46110.27434350.22873919X-RAY DIFFRACTION92
2.4611-2.50350.27064290.23963872X-RAY DIFFRACTION92
2.5035-2.5490.28114570.23874109X-RAY DIFFRACTION97
2.549-2.59810.27194550.24954094X-RAY DIFFRACTION97
2.5981-2.65110.29534590.24864133X-RAY DIFFRACTION97
2.6511-2.70870.27394600.24334138X-RAY DIFFRACTION97
2.7087-2.77180.28064530.24614073X-RAY DIFFRACTION98
2.7718-2.84110.28454550.23964099X-RAY DIFFRACTION98
2.8411-2.91790.28824560.24614104X-RAY DIFFRACTION97
2.9179-3.00380.26934570.24274112X-RAY DIFFRACTION98
3.0038-3.10070.27824610.23214145X-RAY DIFFRACTION98
3.1007-3.21150.25934550.23714099X-RAY DIFFRACTION98
3.2115-3.34010.24874640.22824176X-RAY DIFFRACTION98
3.3401-3.49220.28394540.22794096X-RAY DIFFRACTION98
3.4922-3.67630.33384590.31234128X-RAY DIFFRACTION98
3.6763-3.90660.32434420.26883988X-RAY DIFFRACTION94
3.9066-4.20820.19794550.17774095X-RAY DIFFRACTION97
4.2082-4.63170.17594580.15024120X-RAY DIFFRACTION99
4.6317-5.30180.15964660.14194199X-RAY DIFFRACTION99
5.3018-6.67920.18284630.16534165X-RAY DIFFRACTION99
6.6792-82.01660.17694640.1584178X-RAY DIFFRACTION99
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)
11.98210.0023-0.1230.44710.15360.5443-0.0099-0.4018-0.69270.1054-0.03740.02180.20510.02180.02440.50320.04330.00230.26430.15380.429626.0491-8.603515.7294
22.08740.08420.29560.62760.01590.82160.0104-0.6219-0.06230.1708-0.04410.12610.0646-0.03920.02490.4480.02970.04720.38010.02020.182512.263113.905325.192
32.1895-0.2543-0.08160.7181-0.09360.65080.0666-0.4090.70690.1393-0.031-0.059-0.2090.0443-0.01340.4918-0.00670.01440.2227-0.14140.432327.872746.258210.8594
42.1055-0.03960.05480.90690.1350.56770.01730.41730.7244-0.2153-0.0277-0.0156-0.16970.04080.03490.51880.06040.0190.26970.17710.433326.050246.4841-17.0547
52.29120.09030.31680.91280.16890.83530.00930.8159-0.0661-0.22330.0191-0.14490.06360.0918-0.02540.46810.0780.04990.5107-0.01210.201841.460914.3671-31.8622
62.1114-0.2104-0.12760.8398-0.01850.77560.02750.594-0.6535-0.2088-0.04440.0330.2309-0.00350.01290.53850.0670.00120.3656-0.18720.382827.616-8.1674-22.8686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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