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- PDB-1ykw: Crystal Structure of a Novel RuBisCO-Like Protein from the Green ... -

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Basic information

Entry
Database: PDB / ID: 1ykw
TitleCrystal Structure of a Novel RuBisCO-Like Protein from the Green Sulfur Bacterium Chlorobium tepidum
ComponentsRuBisCO-like protein
KeywordsUNKNOWN FUNCTION / beta-alpha-barrel
Function / homology
Function and homology information


carbon fixation / magnesium ion binding / identical protein binding
Similarity search - Function
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 ...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
Ribulose bisphosphate carboxylase-like protein
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, H. / Sawaya, M.R. / Tabita, F.R. / Eisenberg, D.
CitationJournal: Structure / Year: 2005
Title: Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum.
Authors: Li, H. / Sawaya, M.R. / Tabita, F.R. / Eisenberg, D.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 650HELIX Determination method: Author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RuBisCO-like protein
B: RuBisCO-like protein


Theoretical massNumber of molelcules
Total (without water)96,0512
Polymers96,0512
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-43 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.348, 78.451, 90.369
Angle α, β, γ (deg.)90.00, 99.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSHISHISAA7 - 407 - 40
21LYSLYSHISHISBB7 - 407 - 40
12LYSLYSASNASNAA90 - 16090 - 160
22LYSLYSASNASNBB90 - 16090 - 160
13ALAALAILEILEAA225 - 320225 - 320
23ALAALAILEILEBB225 - 320225 - 320
14GLUGLUVALVALAA333 - 375333 - 375
24GLUGLUVALVALBB333 - 375333 - 375

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein RuBisCO-like protein


Mass: 48025.727 Da / Num. of mol.: 2 / Mutation: M328V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: CT1772 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q8KBL4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG 3350, magnesium formate , pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2003
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2→90 Å / Num. all: 60951 / Num. obs: 60951 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.129 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Num. unique all: 5253 / Rsym value: 0.397 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5RUB

5rub


Resolution: 2→87.71 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.954 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.193 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24539 2956 4.9 %RANDOM
Rwork0.20114 ---
all0.20329 57608 --
obs0.20329 57608 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.441 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å20.67 Å2
2---0.74 Å20 Å2
3---3.15 Å2
Refinement stepCycle: LAST / Resolution: 2→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 0 317 6715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226573
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9648916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16624.31290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.018151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6451533
X-RAY DIFFRACTIONr_chiral_restr0.1170.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025009
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.22874
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24451
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0181.54224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59826639
X-RAY DIFFRACTIONr_scbond_it2.4632637
X-RAY DIFFRACTIONr_scangle_it3.824.52277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1136tight positional0.030.05
2280tight positional0.040.05
3384tight positional0.040.05
4168tight positional0.030.05
1139loose positional0.215
2259loose positional0.235
3351loose positional0.325
4141loose positional0.475
1136tight thermal0.120.5
2280tight thermal0.170.5
3384tight thermal0.170.5
4168tight thermal0.180.5
1139loose thermal0.8510
2259loose thermal0.9910
3351loose thermal1.110
4141loose thermal1.3810
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 161 -
Rwork0.254 3019 -
obs--85.37 %
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)
11.81630.13620.72620.9839-0.21743.5280.02480.45540.4528-0.09160.0108-0.0258-0.2571-0.1322-0.0357-0.03930.050.0174-0.00260.13310.030837.188425.059761.1763
21.9732-0.1111-0.35890.58130.02071.0973-0.04790.2262-0.3297-0.01170.0318-0.04340.22170.09610.0161-0.04970.0182-0.017-0.0803-0.0481-0.036954.3272-3.422173.7012
31.57080.1927-0.82141.25550.05873.5267-0.03490.4798-0.4892-0.11730.0217-0.06120.32710.07810.0133-0.03890.03130.00250.0282-0.14250.011832.6991-11.226261.2429
41.8287-0.20190.31410.6061-0.09591.1205-0.03790.22280.34090.03390.0330.0464-0.2073-0.09250.005-0.05580.01970.0104-0.07340.0455-0.026915.441717.206973.704
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 474 - 47
2X-RAY DIFFRACTION1AA59 - 14459 - 144
3X-RAY DIFFRACTION2AA145 - 428145 - 428
4X-RAY DIFFRACTION3BB4 - 474 - 47
5X-RAY DIFFRACTION3BB59 - 14459 - 144
6X-RAY DIFFRACTION4BB145 - 174145 - 174
7X-RAY DIFFRACTION4BB177 - 428177 - 428

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