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- PDB-6ekc: Crystal structure of the BSD2 homolog of Arabidopsis thaliana bou... -

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Basic information

Entry
Database: PDB / ID: 6ekc
TitleCrystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus
Components
  • DnaJ/Hsp40 cysteine-rich domain superfamily protein
  • Ribulose bisphosphate carboxylase large chain
KeywordsCHAPERONE / zinc finger / assembly chaperone / assembly intermediate
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / : / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding ...ribulose bisphosphate carboxylase complex assembly / : / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone / chloroplast / monooxygenase activity / magnesium ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Heat shock protein DnaJ, cysteine-rich domain superfamily / 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
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.63 Å
AuthorsAigner, H. / Wilson, R.H. / Bracher, A. / Calisse, L. / Bhat, J.Y. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Science / Year: 2017
Title: Plant RuBisCo assembly in E. coli with five chloroplast chaperones including BSD2.
Authors: Aigner, H. / Wilson, R.H. / Bracher, A. / Calisse, L. / Bhat, J.Y. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Ribulose bisphosphate carboxylase large chain
A2: Ribulose bisphosphate carboxylase large chain
A3: Ribulose bisphosphate carboxylase large chain
A4: Ribulose bisphosphate carboxylase large chain
A5: Ribulose bisphosphate carboxylase large chain
A6: Ribulose bisphosphate carboxylase large chain
A7: Ribulose bisphosphate carboxylase large chain
A8: Ribulose bisphosphate carboxylase large chain
C1: Ribulose bisphosphate carboxylase large chain
C2: Ribulose bisphosphate carboxylase large chain
C3: Ribulose bisphosphate carboxylase large chain
C4: Ribulose bisphosphate carboxylase large chain
C5: Ribulose bisphosphate carboxylase large chain
C6: Ribulose bisphosphate carboxylase large chain
C7: Ribulose bisphosphate carboxylase large chain
C8: Ribulose bisphosphate carboxylase large chain
E1: Ribulose bisphosphate carboxylase large chain
E2: Ribulose bisphosphate carboxylase large chain
E3: Ribulose bisphosphate carboxylase large chain
E4: Ribulose bisphosphate carboxylase large chain
E5: Ribulose bisphosphate carboxylase large chain
E6: Ribulose bisphosphate carboxylase large chain
E7: Ribulose bisphosphate carboxylase large chain
E8: Ribulose bisphosphate carboxylase large chain
G1: Ribulose bisphosphate carboxylase large chain
G2: Ribulose bisphosphate carboxylase large chain
G3: Ribulose bisphosphate carboxylase large chain
G4: Ribulose bisphosphate carboxylase large chain
G5: Ribulose bisphosphate carboxylase large chain
G6: Ribulose bisphosphate carboxylase large chain
G7: Ribulose bisphosphate carboxylase large chain
G8: Ribulose bisphosphate carboxylase large chain
I1: Ribulose bisphosphate carboxylase large chain
I2: Ribulose bisphosphate carboxylase large chain
I3: Ribulose bisphosphate carboxylase large chain
I4: Ribulose bisphosphate carboxylase large chain
I5: Ribulose bisphosphate carboxylase large chain
I6: Ribulose bisphosphate carboxylase large chain
I7: Ribulose bisphosphate carboxylase large chain
I8: Ribulose bisphosphate carboxylase large chain
K1: Ribulose bisphosphate carboxylase large chain
K2: Ribulose bisphosphate carboxylase large chain
K3: Ribulose bisphosphate carboxylase large chain
K4: Ribulose bisphosphate carboxylase large chain
K5: Ribulose bisphosphate carboxylase large chain
K6: Ribulose bisphosphate carboxylase large chain
K7: Ribulose bisphosphate carboxylase large chain
K8: Ribulose bisphosphate carboxylase large chain
M1: Ribulose bisphosphate carboxylase large chain
M2: Ribulose bisphosphate carboxylase large chain
M3: Ribulose bisphosphate carboxylase large chain
M4: Ribulose bisphosphate carboxylase large chain
M5: Ribulose bisphosphate carboxylase large chain
M6: Ribulose bisphosphate carboxylase large chain
M7: Ribulose bisphosphate carboxylase large chain
M8: Ribulose bisphosphate carboxylase large chain
O1: Ribulose bisphosphate carboxylase large chain
O2: Ribulose bisphosphate carboxylase large chain
O3: Ribulose bisphosphate carboxylase large chain
O4: Ribulose bisphosphate carboxylase large chain
O5: Ribulose bisphosphate carboxylase large chain
O6: Ribulose bisphosphate carboxylase large chain
O7: Ribulose bisphosphate carboxylase large chain
O8: Ribulose bisphosphate carboxylase large chain
Q1: Ribulose bisphosphate carboxylase large chain
Q2: Ribulose bisphosphate carboxylase large chain
Q3: Ribulose bisphosphate carboxylase large chain
Q4: Ribulose bisphosphate carboxylase large chain
Q5: Ribulose bisphosphate carboxylase large chain
Q6: Ribulose bisphosphate carboxylase large chain
Q7: Ribulose bisphosphate carboxylase large chain
Q8: Ribulose bisphosphate carboxylase large chain
S1: Ribulose bisphosphate carboxylase large chain
S2: Ribulose bisphosphate carboxylase large chain
S3: Ribulose bisphosphate carboxylase large chain
S4: Ribulose bisphosphate carboxylase large chain
S5: Ribulose bisphosphate carboxylase large chain
S6: Ribulose bisphosphate carboxylase large chain
S7: Ribulose bisphosphate carboxylase large chain
S8: Ribulose bisphosphate carboxylase large chain
B1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,921,405320
Polymers4,910,939160
Non-polymers10,465160
Water11,043613
1
A1: Ribulose bisphosphate carboxylase large chain
A2: Ribulose bisphosphate carboxylase large chain
A3: Ribulose bisphosphate carboxylase large chain
A4: Ribulose bisphosphate carboxylase large chain
A5: Ribulose bisphosphate carboxylase large chain
A6: Ribulose bisphosphate carboxylase large chain
A7: Ribulose bisphosphate carboxylase large chain
A8: Ribulose bisphosphate carboxylase large chain
B1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
B8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C1: Ribulose bisphosphate carboxylase large chain
C2: Ribulose bisphosphate carboxylase large chain
C3: Ribulose bisphosphate carboxylase large chain
C4: Ribulose bisphosphate carboxylase large chain
C5: Ribulose bisphosphate carboxylase large chain
C6: Ribulose bisphosphate carboxylase large chain
C7: Ribulose bisphosphate carboxylase large chain
C8: Ribulose bisphosphate carboxylase large chain
D1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
D8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E1: Ribulose bisphosphate carboxylase large chain
E2: Ribulose bisphosphate carboxylase large chain
E3: Ribulose bisphosphate carboxylase large chain
E4: Ribulose bisphosphate carboxylase large chain
E5: Ribulose bisphosphate carboxylase large chain
E6: Ribulose bisphosphate carboxylase large chain
E7: Ribulose bisphosphate carboxylase large chain
E8: Ribulose bisphosphate carboxylase large chain
F1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
F8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G1: Ribulose bisphosphate carboxylase large chain
G2: Ribulose bisphosphate carboxylase large chain
G3: Ribulose bisphosphate carboxylase large chain
G4: Ribulose bisphosphate carboxylase large chain
G5: Ribulose bisphosphate carboxylase large chain
G6: Ribulose bisphosphate carboxylase large chain
G7: Ribulose bisphosphate carboxylase large chain
G8: Ribulose bisphosphate carboxylase large chain
H1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
H8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I1: Ribulose bisphosphate carboxylase large chain
I2: Ribulose bisphosphate carboxylase large chain
I3: Ribulose bisphosphate carboxylase large chain
I4: Ribulose bisphosphate carboxylase large chain
I5: Ribulose bisphosphate carboxylase large chain
I6: Ribulose bisphosphate carboxylase large chain
I7: Ribulose bisphosphate carboxylase large chain
I8: Ribulose bisphosphate carboxylase large chain
J1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
J8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K1: Ribulose bisphosphate carboxylase large chain
K2: Ribulose bisphosphate carboxylase large chain
K3: Ribulose bisphosphate carboxylase large chain
K4: Ribulose bisphosphate carboxylase large chain
K5: Ribulose bisphosphate carboxylase large chain
K6: Ribulose bisphosphate carboxylase large chain
K7: Ribulose bisphosphate carboxylase large chain
K8: Ribulose bisphosphate carboxylase large chain
L1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
L8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M1: Ribulose bisphosphate carboxylase large chain
M2: Ribulose bisphosphate carboxylase large chain
M3: Ribulose bisphosphate carboxylase large chain
M4: Ribulose bisphosphate carboxylase large chain
M5: Ribulose bisphosphate carboxylase large chain
M6: Ribulose bisphosphate carboxylase large chain
M7: Ribulose bisphosphate carboxylase large chain
M8: Ribulose bisphosphate carboxylase large chain
N1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
N8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O1: Ribulose bisphosphate carboxylase large chain
O2: Ribulose bisphosphate carboxylase large chain
O3: Ribulose bisphosphate carboxylase large chain
O4: Ribulose bisphosphate carboxylase large chain
O5: Ribulose bisphosphate carboxylase large chain
O6: Ribulose bisphosphate carboxylase large chain
O7: Ribulose bisphosphate carboxylase large chain
O8: Ribulose bisphosphate carboxylase large chain
P1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
P8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Q1: Ribulose bisphosphate carboxylase large chain
Q2: Ribulose bisphosphate carboxylase large chain
Q3: Ribulose bisphosphate carboxylase large chain
Q4: Ribulose bisphosphate carboxylase large chain
Q5: Ribulose bisphosphate carboxylase large chain
Q6: Ribulose bisphosphate carboxylase large chain
Q7: Ribulose bisphosphate carboxylase large chain
Q8: Ribulose bisphosphate carboxylase large chain
R1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
R8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S1: Ribulose bisphosphate carboxylase large chain
S2: Ribulose bisphosphate carboxylase large chain
S3: Ribulose bisphosphate carboxylase large chain
S4: Ribulose bisphosphate carboxylase large chain
S5: Ribulose bisphosphate carboxylase large chain
S6: Ribulose bisphosphate carboxylase large chain
S7: Ribulose bisphosphate carboxylase large chain
S8: Ribulose bisphosphate carboxylase large chain
T1: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T2: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T3: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T4: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T5: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T6: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T7: DnaJ/Hsp40 cysteine-rich domain superfamily protein
T8: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,14032
Polymers491,09416
Non-polymers1,04716
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)217.918, 218.592, 310.273
Angle α, β, γ (deg.)69.400, 81.510, 65.500
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 53031.273 Da / Num. of mol.: 80 / Fragment: RbcL / Mutation: F345I / P415A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: cbbL, rbcL, tll1506 / Plasmid: pCDF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8DIS5, ribulose-bisphosphate carboxylase
#2: Protein ...
DnaJ/Hsp40 cysteine-rich domain superfamily protein / Uncharacterized protein At3g47650 / Uncharacterized protein F1P2.200


Mass: 8355.468 Da / Num. of mol.: 80 / Fragment: mature protein, residues 53-136 / Mutation: K56M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F1P2.200, At3g47650 / Plasmid: pCDF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SN73
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 160 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 21 % PEG 3350 and 0.12M DL-malic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.63→198.29 Å / Num. obs: 1427774 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.09 / Rrim(I) all: 0.171 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.63-2.673.71.215703980.4310.7371.42498.2
14.41-198.293.60.0486760.9990.0240.04798.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.614
Highest resolutionLowest resolution
Rotation188.71 Å3 Å

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
MOLREP11.4.06phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSJun 1, 2017data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZXW

3zxw


Resolution: 2.63→50.01 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 18.454 / SU ML: 0.357 / SU R Cruickshank DPI: 1.3685 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.369 / ESU R Free: 0.359
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2742 71428 5 %RANDOM
Rwork0.2355 ---
obs0.2375 1356119 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 197.43 Å2 / Biso mean: 57.241 Å2 / Biso min: 7.91 Å2
Refinement stepCycle: final / Resolution: 2.63→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms321026 0 160 613 321799
Biso mean--70.45 27.63 -
Num. residues----41600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019328426
X-RAY DIFFRACTIONr_bond_other_d0.0020.02308412
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.948444862
X-RAY DIFFRACTIONr_angle_other_deg0.8893708344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.936541440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22523.66915036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2361553354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.87152240
X-RAY DIFFRACTIONr_chiral_restr0.0630.248000
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021377424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0277760
LS refinement shellResolution: 2.63→2.698 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 5239 -
Rwork0.362 99801 -
all-105040 -
obs--98.18 %

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