[English] 日本語
Yorodumi
- PDB-1uzd: Chlamydomonas,Spinach Chimeric Rubisco -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uzd
TitleChlamydomonas,Spinach Chimeric Rubisco
Components(Ribulose bisphosphate carboxylase ...) x 2
KeywordsLYASE / 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 / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain ...Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / 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 large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Spinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKarkehabadi, S. / Spreitzer, R.J. / Andersson, I.
CitationJournal: 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
DepositionMar 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 4, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_database_status / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity.src_method / _entity_name_com.name / _pdbx_database_status.status_code_sf / _pdbx_struct_mod_residue.details / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic
E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic
H: Ribulose bisphosphate carboxylase large chain
I: Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic
J: Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic
K: Ribulose bisphosphate carboxylase large chain
M: Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic
O: Ribulose bisphosphate carboxylase large chain
P: Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic
R: Ribulose bisphosphate carboxylase large chain
T: Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic
V: Ribulose bisphosphate carboxylase large chain
W: Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)553,73886
Polymers547,34316
Non-polymers6,39570
Water34,0661891
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)220.014, 224.078, 111.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9447, 0.3198, 0.07214), (0.3198, -0.9474, 0.01178), (0.07211, 0.01194, -0.9973)-13.04, 67.49, 51.69
2given(-0.3208, 0.9471, 0.003269), (0.9471, 0.3208, 0.003249), (0.002028, 0.004139, -1)43.13, -31.23, 56.75
3given(-0.9472, -0.3203, 0.01054), (-0.3203, 0.9449, -0.06715), (0.01155, -0.06698, -0.9977)141.89999, 25.25, 59.24
4given(-0.001938, 0.9976, -0.06864), (-0.9999, -0.002908, -0.01403), (-0.0142, 0.0686, 0.9975)22.02, 111.6, -2.154
5given(0.008612, -0.9999, -0.0149), (0.9976, 0.007575, 0.06828), (-0.06816, -0.01546, 0.9976)111.1, -22.13, 5.268
6given(-0.9965, -0.006193, -0.08382), (0.001507, -0.9984, 0.05585), (-0.08404, 0.05553, 0.9949)133.39999, 89.54, 3.158
7given(0.3219, -0.9435, 0.07911), (-0.9433, -0.3267, -0.05775), (0.08033, -0.05604, -0.9952)85.28, 124, 54.15
8given(0.9424, 0.3265, 0.07281), (0.3268, -0.9451, 0.008759), (0.07167, 0.01554, -0.9973)-13.24, 67.14, 51.56
9given(-0.3227, 0.9465, 0.002013), (0.9465, 0.3227, 0.000834), (0.00014, 0.002175, -1)43.32, -31.17, 56.9
10given(-0.9464, -0.3227, 0.01548), (-0.3229, 0.9439, -0.069), (0.007651, -0.0703, -0.9975)141.89999, 25.55, 59.76
11given(-0.000736, 0.9975, -0.07039), (-0.9999, -0.001476, -0.01046), (-0.01054, 0.07038, 0.9975)22.04, 111.4, -2.446
12given(0.002121, -0.9999, -0.01548), (0.9974, 0.000993, 0.07247), (-0.07245, -0.01559, 0.9973)111.5, -21.92, 5.545
13given(-0.9967, -0.001846, -0.08138), (-0.002854, -0.9983, 0.05759), (-0.08135, 0.05763, 0.995)133.10001, 89.83, 2.803
14given(0.3225, -0.9433, 0.07878), (-0.9432, -0.3272, -0.05743), (0.07995, -0.05579, -0.9952)85.22, 124.1, 54.2
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

-
Components

-
Ribulose bisphosphate carboxylase ... , 2 types, 16 molecules ABEHKORVCFIJMPTW

#1: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


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
Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic / RuBisCO small subunit 2 / RuBisCO small subunit 1


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

-
Sugars , 1 types, 8 molecules

#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2

-
Non-polymers , 3 types, 1953 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1891 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsRUBISCO CATALYZES TWO REACTIONS: THE CARBOXYLATION OF D- RIBULOSE 1,5-BISPHOSPHATE, THE PRIMARY ...RUBISCO CATALYZES TWO REACTIONS: THE CARBOXYLATION OF D- RIBULOSE 1,5-BISPHOSPHATE, THE PRIMARY EVENT IN PHOTOSYNTHETIC CARBON DIOXIDE FIXATION, AS WELL AS THE OXIDATIVE FRAGMENTATION OF THE PENTOSE SUBSTRATE IN THE PHOTORESPIRATION PROCESS. BOTH REACTIONS OCCUR SIMULTANEOUSLY AND IN COMPETITION AT THE SAME ACTIVE SITE.
Sequence detailsTHE SMALL SUBUNIT LOOP BA-BB OF CHLAMYDOMONAS RUBISCO, (RESIDUES 46 - 70 ;EADKAYVSNESAIRFGSVSCLYYDN) ...THE SMALL SUBUNIT LOOP BA-BB OF CHLAMYDOMONAS RUBISCO, (RESIDUES 46 - 70 ;EADKAYVSNESAIRFGSVSCLYYDN) IS 6 RESIDUES LONGER THAN THE CORRESPONDING LOOP OF SPINACH RUBISCO ( RESIDUES 46 - 64; TDHGFVYREHHNSPGYYDG. THE REPLACEMENT OF CHLMYDOMONAS RUBISCO LOOP WITH SPINACH RUBISCO LOOP AFFECTS THE NUMBERING OF THE SMALL SUBUNIT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / % possible all: 96

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GK8

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
RfactorNum. reflection% reflectionSelection details
Rfree0.23 10097 5 %RANDOM
Rwork0.1884 ---
obs0.19 190692 93.3 %-
Displacement parametersBiso mean: 20.921 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.29 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37624 0 392 1891 39907

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more