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- PDB-3wqp: Crystal structure of Rubisco T289D mutant from Thermococcus kodak... -

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Basic information

Entry
Database: PDB / ID: 3wqp
TitleCrystal structure of Rubisco T289D mutant from Thermococcus kodakarensis
ComponentsRibulose bisphosphate carboxylase
KeywordsLYASE / decamer / protein-ligand complex
Function / homology
Function and homology information


AMP catabolic process / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / oxidoreductase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, type III / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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 ...Ribulose bisphosphate carboxylase, type III / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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 speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsFujihashi, M. / Nishitani, Y. / Kiriyama, T. / Miki, K.
CitationJournal: to be published
Title: Mutation design of thermophilic Rubisco based on the three-dimensional structure enhances its activity at ambient temperature
Authors: Kiriyama, T. / Fujihashi, M. / Nishitani, Y. / Aono, R. / Sato, T. / Takai, T. / Tagashira, K. / Fukuda, W. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionJan 29, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 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

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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
G: Ribulose bisphosphate carboxylase
H: Ribulose bisphosphate carboxylase
I: Ribulose bisphosphate carboxylase
J: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)502,76040
Polymers498,33510
Non-polymers4,42530
Water36,2282011
1
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
E: Ribulose bisphosphate carboxylase
hetero molecules

A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
E: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)502,76040
Polymers498,33510
Non-polymers4,42530
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area65390 Å2
ΔGint-346 kcal/mol
Surface area126270 Å2
MethodPISA
2
F: Ribulose bisphosphate carboxylase
G: Ribulose bisphosphate carboxylase
H: Ribulose bisphosphate carboxylase
I: Ribulose bisphosphate carboxylase
J: Ribulose bisphosphate carboxylase
hetero molecules

F: Ribulose bisphosphate carboxylase
G: Ribulose bisphosphate carboxylase
H: Ribulose bisphosphate carboxylase
I: Ribulose bisphosphate carboxylase
J: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)502,76040
Polymers498,33510
Non-polymers4,42530
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area65560 Å2
ΔGint-346 kcal/mol
Surface area126270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.566, 246.238, 144.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11I-651-

HOH

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Components

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO / Ribulose-1 / 5-bisphosphate carboxylase/decarboxylase


Mass: 49833.465 Da / Num. of mol.: 10 / Mutation: T289D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: rbcL, rbc, TK2290 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS
References: UniProt: O93627, ribulose-bisphosphate carboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O13P2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2011 / 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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: Sodium Acetate 100mM (pH6.0), PEG 6000 5%(w/v), 2-methyl-1,4-pentanediol 10%(v/v), Calcium Chloride 120mM, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationMonochromator: default / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 287149 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rsym value: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3A12

3a12


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 15.283 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 14396 5 %RANDOM
Rwork0.2201 ---
obs0.222 286386 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.08 Å2 / Biso mean: 51.496 Å2 / Biso min: 11.03 Å2
Baniso -1Baniso -2Baniso -3
1-8.45 Å20 Å20 Å2
2---4.19 Å20 Å2
3----4.26 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34306 0 260 2011 36577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01935432
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.96148076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.10854359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86923.6141638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.001155645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7815220
X-RAY DIFFRACTIONr_chiral_restr0.0690.25065
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02127302
LS refinement shellResolution: 2.249→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 1025 -
Rwork0.33 19027 -
all-20052 -
obs--98.77 %
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)
10.55140.0234-0.2541.22170.25021.71210.0368-0.0322-0.0757-0.5587-0.0810.2859-0.4004-0.23320.04420.3860.1292-0.14720.219-0.01780.266478.202644.9261.4773
20.8544-0.3366-0.1171.63980.39541.4708-0.076-0.034-0.0325-0.7826-0.00860.262-0.0766-0.22850.08460.70490.0608-0.16790.17140.00730.137271.9699-1.3492-28.3597
30.4786-0.13760.14911.3926-0.35211.43450.025-0.00780.0172-0.45010.0710.20590.2846-0.2654-0.0960.2755-0.0391-0.07450.2950.02180.257566.2983-43.45247.5879
40.86740.22480.39592.0938-0.03871.18150.02650.0849-0.0490.95390.07440.4202-0.3412-0.1737-0.10090.52820.05870.22760.27530.02850.319368.8465-23.02759.4709
50.85870.6257-0.25841.9446-0.0091.0560.13290.11470.08640.694-0.04830.3552-0.0704-0.1594-0.08460.28590.03810.14410.26020.00750.302576.55831.806555.915
60.56590.16380.38711.5943-0.3872.36-0.0485-0.02680.062-0.8411-0.2155-0.30220.83530.37580.2640.70470.24530.31260.22280.08930.24547.355-44.901646.4117
70.7655-0.26130.12321.3051-0.30062.1163-0.0959-0.04430.0438-0.4546-0.0696-0.21610.01830.35760.16550.57030.06030.11060.20420.03110.172513.25771.523516.2189
80.4768-0.1614-0.14661.48280.83911.966-0.03870.0134-0.0458-0.64750.0825-0.2695-0.70610.4043-0.04380.5271-0.12350.03470.27750.01530.23419.023143.502552.2432
90.85310.3076-0.46762.36120.24611.51390.00510.093-0.01770.8039-0.0272-0.33090.30410.14640.02210.34010.0098-0.19910.2670.02470.316616.561823.0378104.1213
100.69380.59390.11891.9633-0.11230.86160.05810.0283-0.03720.4124-0.1402-0.36280.06450.16670.08210.15620.0148-0.00570.290.04330.32568.7787-31.785100.504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 444
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION2B7 - 444
4X-RAY DIFFRACTION2B501 - 502
5X-RAY DIFFRACTION3C7 - 444
6X-RAY DIFFRACTION3C501 - 502
7X-RAY DIFFRACTION4D9 - 444
8X-RAY DIFFRACTION4D501 - 502
9X-RAY DIFFRACTION5E7 - 444
10X-RAY DIFFRACTION5E501 - 502
11X-RAY DIFFRACTION6F9 - 444
12X-RAY DIFFRACTION6F501 - 502
13X-RAY DIFFRACTION7G9 - 444
14X-RAY DIFFRACTION7G501 - 502
15X-RAY DIFFRACTION8H8 - 444
16X-RAY DIFFRACTION8H501 - 502
17X-RAY DIFFRACTION9I9 - 444
18X-RAY DIFFRACTION9I501 - 502
19X-RAY DIFFRACTION10J8 - 444
20X-RAY DIFFRACTION10J501 - 502

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