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- PDB-5hql: Structure function studies of R. palustris RubisCO (A47V-M331A mu... -

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Basic information

Entry
Database: PDB / ID: 5hql
TitleStructure function studies of R. palustris RubisCO (A47V-M331A mutant; CABP-bound; no expression tag)
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: 2.53 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. / Shin, A. / Cascio, D. / 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 1.2Mar 21, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 1.5Nov 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)305,60618
Polymers303,3246
Non-polymers2,28312
Water6,539363
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.443, 100.491, 103.965
Angle α, β, γ (deg.)108.130, 113.660, 95.440
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: MG / End label comp-ID: MG / Auth seq-ID: 1 - 501 / Label seq-ID: 1

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - H
2chain BBB - J
3chain CCC - L
4chain DDD - N
5chain EEE - P
6chain FFF - R

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Components

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO


Mass: 50553.934 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.: 363 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Reservoir solution: 20-24% PEG 3350, 200 mM sodium sulfate, 100 mM Bis-Tris Propane pH 7.0-8.0. Protein storage buffer: 20 mM Tris, pH 8.0, 300 mM NaCl, 10% Glycerol, 10 mM MgCl2, 20 mM NaHCO3.
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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.53→87.961 Å / Num. obs: 77023 / % possible obs: 90.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 37.29 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.116 / Net I/σ(I): 4.3 / Num. measured all: 214324
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.53-2.662.40.6971.226186110130.6340.53688.3
7.99-92.343.50.09411.5839223930.9740.0689.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.27data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LF1

4lf1


Resolution: 2.53→87.961 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 7700 10 %Random selection
Rwork0.2134 69302 --
obs0.2179 77002 90.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.55 Å2 / Biso mean: 48.9669 Å2 / Biso min: 9.95 Å2
Refinement stepCycle: final / Resolution: 2.53→87.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20920 0 132 363 21415
Biso mean--45.45 30.22 -
Num. residues----2735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521572
X-RAY DIFFRACTIONf_angle_d1.03829257
X-RAY DIFFRACTIONf_chiral_restr0.0473076
X-RAY DIFFRACTIONf_plane_restr0.0053874
X-RAY DIFFRACTIONf_dihedral_angle_d11.5837601
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16091X-RAY DIFFRACTION12.142TORSIONAL
12B16091X-RAY DIFFRACTION12.142TORSIONAL
13C16091X-RAY DIFFRACTION12.142TORSIONAL
14D16091X-RAY DIFFRACTION12.142TORSIONAL
15E16091X-RAY DIFFRACTION12.142TORSIONAL
16F16091X-RAY DIFFRACTION12.142TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.53-2.55880.32532620.28042356261892
2.5588-2.58890.36472640.28712369263393
2.5889-2.62040.29742550.28422292254792
2.6204-2.65360.34822670.28372403267092
2.6536-2.68850.30882500.26932250250091
2.6885-2.72540.30362610.26172351261291
2.7254-2.76430.30892510.27762262251389
2.7643-2.80560.33632430.26082186242986
2.8056-2.84940.28982420.25822180242286
2.8494-2.89610.29862650.25992384264994
2.8961-2.94610.3322650.26162381264694
2.9461-2.99960.29962650.24562391265694
2.9996-3.05730.28282670.24112395266294
3.0573-3.11980.29922600.25132348260893
3.1198-3.18760.28162600.2392339259993
3.1876-3.26170.29082630.23482364262792
3.2617-3.34330.30362530.24272275252890
3.3433-3.43370.30082440.24462195243987
3.4337-3.53480.25872480.22742234248287
3.5348-3.64890.27112650.20422386265195
3.6489-3.77930.2082630.19372365262894
3.7793-3.93060.2442640.19132383264793
3.9306-4.10950.22912620.18242355261793
4.1095-4.32610.21862550.17242297255290
4.3261-4.59720.20462340.16452102233682
4.5972-4.95210.19632610.16842349261093
4.9521-5.45040.21212590.17032328258792
5.4504-6.23890.25382570.18892325258291
6.2389-7.85950.23312460.18632213245988
7.8595-88.01370.22312490.19332244249388
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)
10.7791-0.04120.17060.8908-0.01290.6522-0.0035-0.24190.06080.3003-0.0150.11870.0186-0.11890.02960.44870.01240.04220.3428-0.01080.236-27.81014.492913.8544
20.93410.0126-0.21810.8194-0.10610.99030.0848-0.1519-0.12410.1923-0.01790.05770.2370.0545-0.05830.49510.0076-0.04040.24970.03580.2672-23.7867-20.87172.7304
30.8761-0.2977-0.12990.92860.10540.66560.0463-0.06710.125-0.0579-0.0137-0.1013-0.10240.185-0.02450.33990.00080.02110.2731-0.0220.2646-14.118931.9119-9.569
41.3024-0.149-0.4011.16470.15250.8350.01630.1369-0.1843-0.0585-0.03030.12540.0616-0.10910.020.34680.0246-0.04470.2127-0.00570.2891-38.4892-22.4291-32.7369
50.8065-0.0489-0.01210.98260.10840.6397-0.00190.07410.1973-0.2347-0.03550.0394-0.1928-0.00460.03940.3870.03960.00290.24160.03470.2422-27.214931.2964-34.19
60.85620.18720.221.28180.18490.9034-0.05280.2528-0.0332-0.53050.0429-0.1302-0.00720.0848-00.50650.03510.04930.29930.01630.2564-26.2296-4.1548-49.1715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A1 - 501
2X-RAY DIFFRACTION2chain 'B'B1 - 501
3X-RAY DIFFRACTION3chain 'C'C1 - 501
4X-RAY DIFFRACTION4chain 'D'D1 - 501
5X-RAY DIFFRACTION5chain 'E'E1 - 501
6X-RAY DIFFRACTION6chain 'F'F1 - 501

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