+Open data
-Basic information
Entry | Database: PDB / ID: 1uzd | ||||||
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Title | Chlamydomonas,Spinach Chimeric Rubisco | ||||||
Components | (Ribulose bisphosphate carboxylase ...) x 2 | ||||||
Keywords | LYASE / RUBISCO / PHOTOSYNTHESIS / CARBON DIOXIDE FIXATION / PHOTORESPIRATION / OXIDOREDUCTASE / MONOOXYGENASE / CHLOROPLAST / TRANSIT PEPTIDE / MULTIGENE FAMILY | ||||||
Function / homology | Function and homology information photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Karkehabadi, S. / Spreitzer, R.J. / Andersson, I. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Chimeric Small Subunits Influence Catalysis without Causing Global Conformational Changes in the Crystal Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Authors: Karkehabadi, S. / Peddi, S.R. / Anwaruzzaman, M. / Taylor, T.C. / Cederlund, A. / Genkov, T. / Andersson, I. / Spreitzer, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uzd.cif.gz | 953.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uzd.ent.gz | 796.1 KB | Display | PDB format |
PDBx/mmJSON format | 1uzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uzd_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 1uzd_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 1uzd_validation.xml.gz | 190.6 KB | Display | |
Data in CIF | 1uzd_validation.cif.gz | 261.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/1uzd ftp://data.pdbj.org/pub/pdb/validation_reports/uz/1uzd | HTTPS FTP |
-Related structure data
Related structure data | 1uzhC 1gk8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 |
-Components
-Ribulose bisphosphate carboxylase ... , 2 types, 16 molecules ABEHKORVCFIJMPTW
#1: Protein | Mass: 52696.840 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) References: UniProt: A0A218N8A3, UniProt: P00877*PLUS, ribulose-bisphosphate carboxylase #2: Protein | Mass: 15721.088 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: ONE LOOP OF CHLAMYDOMONAS RUBISCO, RESIDUES GLU46-ASN70 HAS BEEN REPLACED WITH THE CORRESPONDING LOOP FROM SPINACH RUBISCO, RESIDUES THR46 - GLY64,ONE LOOP OF CHLAMYDOMONAS RUBISCO, RESIDUES ...Details: ONE LOOP OF CHLAMYDOMONAS RUBISCO, RESIDUES GLU46-ASN70 HAS BEEN REPLACED WITH THE CORRESPONDING LOOP FROM SPINACH RUBISCO, RESIDUES THR46 - GLY64,ONE LOOP OF CHLAMYDOMONAS RUBISCO, RESIDUES GLU46-ASN70 HAS BEEN REPLACED WITH THE CORRESPONDING LOOP FROM SPINACH RUBISCO, RESIDUES THR46 - GLY64 Source: (gene. exp.) Chlamydomonas reinhardtii (plant), (gene. exp.) Spinacia oleracea (spinach) Gene: RBCS-1, CHLRE_02g120100v5, CHLREDRAFT_82986, RBCS2 / Production host: Chlamydomonas reinhardtii (plant) References: UniProt: P00873, UniProt: Q43832, ribulose-bisphosphate carboxylase |
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-Sugars , 1 types, 8 molecules
#4: Sugar | ChemComp-CAP / |
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-Non-polymers , 3 types, 1953 molecules
#3: Chemical | ChemComp-MG / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | RUBISCO CATALYZES TWO REACTIONS: THE CARBOXYLATION OF D- RIBULOSE 1,5-BISPHOSPHATE, THE PRIMARY ...RUBISCO CATALYZES TWO REACTIONS: THE CARBOXYLAT |
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Sequence details | THE SMALL SUBUNIT LOOP BA-BB OF CHLAMYDOMONAS RUBISCO, (RESIDUES 46 - 70 ;EADKAYVSNESAIRFGSVSCLYYDN) ...THE SMALL SUBUNIT LOOP BA-BB OF CHLAMYDOMO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 50 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 215895 / % possible obs: 95.4 % / Redundancy: 29.8 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GK8 Resolution: 2.4→50 Å / SU B: 8.838 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.264
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Displacement parameters | Biso mean: 20.921 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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