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- PDB-1tel: Crystal structure of a RubisCO-like protein from Chlorobium tepidum -

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Basic information

Entry
Database: PDB / ID: 1tel
TitleCrystal structure of a RubisCO-like protein from Chlorobium tepidum
Componentsribulose bisphosphate carboxylase, large subunit
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RubisCO-like protein / NYSGXRC / target 1798 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
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 speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a RubisCO-like protein from Chlorobium tepidum
Authors: Fedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.
History
DepositionMay 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribulose bisphosphate carboxylase, large subunit
B: ribulose bisphosphate carboxylase, large subunit


Theoretical massNumber of molelcules
Total (without water)96,1162
Polymers96,1162
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-53 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.105, 77.708, 88.758
Angle α, β, γ (deg.)90.00, 99.57, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer

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Components

#1: Protein ribulose bisphosphate carboxylase, large subunit


Mass: 48057.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Species: Chlorobaculum tepidum / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KBL4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.39 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, Tris HCl, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.97938, 0.97919, 0.96408
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 21, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979381
20.979191
30.964081
ReflectionResolution: 2.7→25 Å / Num. all: 24718 / Num. obs: 24718 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 1198 RANDOM
Rwork0.209 --
all0.212 24718 -
obs0.212 24718 -
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 0 47 6651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d23.89
X-RAY DIFFRACTIONc_improper_angle_d0.853
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4cis_peptide.param

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