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- PDB-5hjy: Structure function studies of R. palustris RubisCO (I165T mutant;... -

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Basic information

Entry
Database: PDB / ID: 5hjy
TitleStructure function studies of R. palustris RubisCO (I165T mutant; CABP-bound)
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 / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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 / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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: 2.3 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. / Shin, 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)318,79019
Polymers316,4726
Non-polymers2,31813
Water24,7171372
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.860, 100.020, 103.560
Angle α, β, γ (deg.)107.84, 113.77, 96.09
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: 52745.289 Da / Num. of mol.: 6 / Mutation: I165T
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1372 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
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: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→91.85 Å / Num. obs: 103448 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 25.86 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.99
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.76 / % possible all: 90

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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: 2.3→91.85 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 10342 10 %Random selection
Rwork0.183 ---
obs0.187 103417 93.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.82 Å2
Refinement stepCycle: LAST / Resolution: 2.3→91.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21068 0 133 1372 22573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621785
X-RAY DIFFRACTIONf_angle_d0.84429459
X-RAY DIFFRACTIONf_dihedral_angle_d11.9547809
X-RAY DIFFRACTIONf_chiral_restr0.0343061
X-RAY DIFFRACTIONf_plane_restr0.0043904
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A16150X-RAY DIFFRACTIONPOSITIONAL
12B16150X-RAY DIFFRACTIONPOSITIONAL
13C16150X-RAY DIFFRACTIONPOSITIONAL
14D16150X-RAY DIFFRACTIONPOSITIONAL
15E16150X-RAY DIFFRACTIONPOSITIONAL
16F16150X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2992-2.32530.29843180.24462859X-RAY DIFFRACTION86
2.3253-2.35270.27773450.22533107X-RAY DIFFRACTION94
2.3527-2.38140.28343480.22453131X-RAY DIFFRACTION93
2.3814-2.41150.26333430.21763083X-RAY DIFFRACTION93
2.4115-2.44330.28063430.22173091X-RAY DIFFRACTION92
2.4433-2.47670.28593280.22972955X-RAY DIFFRACTION90
2.4767-2.51210.26033250.21512926X-RAY DIFFRACTION88
2.5121-2.54960.25943540.21343176X-RAY DIFFRACTION96
2.5496-2.58950.25063490.21763145X-RAY DIFFRACTION96
2.5895-2.63190.2933550.21663198X-RAY DIFFRACTION95
2.6319-2.67730.23353550.21013188X-RAY DIFFRACTION96
2.6773-2.7260.26923510.21343163X-RAY DIFFRACTION95
2.726-2.77840.27153500.21153148X-RAY DIFFRACTION95
2.7784-2.83510.27633510.20663166X-RAY DIFFRACTION95
2.8351-2.89680.25953460.2033117X-RAY DIFFRACTION95
2.8968-2.96420.27553500.20763155X-RAY DIFFRACTION94
2.9642-3.03830.24143470.20443124X-RAY DIFFRACTION94
3.0383-3.12050.25843400.19983062X-RAY DIFFRACTION92
3.1205-3.21230.24763320.19632985X-RAY DIFFRACTION90
3.2123-3.3160.23873290.19352956X-RAY DIFFRACTION89
3.316-3.43450.2233550.1863197X-RAY DIFFRACTION96
3.4345-3.5720.22773570.17673207X-RAY DIFFRACTION96
3.572-3.73460.19993510.16353161X-RAY DIFFRACTION96
3.7346-3.93150.19693520.15593168X-RAY DIFFRACTION95
3.9315-4.17780.17983500.14713147X-RAY DIFFRACTION94
4.1778-4.50040.16983390.14453052X-RAY DIFFRACTION92
4.5004-4.95320.16073260.13862937X-RAY DIFFRACTION88
4.9532-5.66990.193570.15093217X-RAY DIFFRACTION97
5.6699-7.1430.19143560.16523196X-RAY DIFFRACTION96
7.143-91.850.18413400.16973058X-RAY DIFFRACTION92
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)
11.195-0.3614-0.10640.67770.090.561-0.018-0.15270.20990.03860.0636-0.1013-0.11140.1229-0.04440.2406-0.0094-0.00480.1851-0.05450.15731.49285.2372-1.8819
21.43020.0805-0.01610.50760.14360.5268-0.0050.16260.2127-0.1474-0.0010.0337-0.13170.01950.00450.25730.0133-0.00370.13560.01740.148618.41584.5603-26.4645
30.95860.1290.08860.98920.07840.5247-0.04550.3081-0.0842-0.36180.0575-0.03110.02920.0431-0.01410.34270.00860.00510.216-0.02910.14220.058-30.8112-41.7163
41.4298-0.2119-0.3910.86040.12950.6273-0.01240.1123-0.2706-0.0894-0.00170.11380.1232-0.06910.01370.2502-0.001-0.0460.1368-0.00980.19797.4276-49.1215-25.0879
51.53160.0226-0.19010.55350.17850.56950.0033-0.2556-0.26690.20420.00430.040.25760.068-0.0150.43410.0103-0.02820.18170.05430.189522.0265-47.433910.4286
60.84920.07830.17110.61040.02250.54480.0289-0.3330.05720.3183-0.01540.05330.0903-0.047-0.01450.3778-0.02390.0260.2882-0.02880.135517.7916-22.23721.4676
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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