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- PDB-6l8d: Hexameric structure of the ATPase subunit of magnesium chelatase -

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Basic information

Entry
Database: PDB / ID: 6l8d
TitleHexameric structure of the ATPase subunit of magnesium chelatase
ComponentsMagnesium-chelatase subunit ChlI
KeywordsHYDROLASE / AAA+ / ATPase / Magnesium chelatase / chlorophyll biosynthesis
Function / homology
Function and homology information


magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / ATP hydrolysis activity / ATP binding
Similarity search - Function
Magnesium chelatase, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Magnesium-chelatase subunit ChlI
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsGao, Y. / Liu, L.
CitationJournal: Protein Sci. / Year: 2020
Title: Hexameric structure of the ATPase motor subunit of magnesium chelatase in chlorophyll biosynthesis.
Authors: Gao, Y.S. / Wang, Y.L. / Wang, X. / Liu, L.
History
DepositionNov 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magnesium-chelatase subunit ChlI
B: Magnesium-chelatase subunit ChlI
C: Magnesium-chelatase subunit ChlI
D: Magnesium-chelatase subunit ChlI
E: Magnesium-chelatase subunit ChlI
F: Magnesium-chelatase subunit ChlI


Theoretical massNumber of molelcules
Total (without water)243,5006
Polymers243,5006
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-28 kcal/mol
Surface area75650 Å2
Unit cell
Length a, b, c (Å)211.034, 121.149, 119.419
Angle α, β, γ (deg.)90.000, 99.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESID 14 THROUGH 46 OR RESID 53...
21(CHAIN B AND (RESID 14 THROUGH 46 OR RESID 53...
31(CHAIN C AND (RESID 14 THROUGH 46 OR RESID 53...
41(CHAIN D AND (RESID 14 THROUGH 46 OR RESID 53...
51(CHAIN E AND (RESID 14 THROUGH 46 OR RESID 53...
61(CHAIN F AND (RESID 14 THROUGH 46 OR RESID 53...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVAL(CHAIN A AND (RESID 14 THROUGH 46 OR RESID 53...AA1414
12LYSLYSLYSLYS(CHAIN A AND (RESID 14 THROUGH 46 OR RESID 53...AA5353
13GLUGLUGLUGLU(CHAIN A AND (RESID 14 THROUGH 46 OR RESID 53...AA6666
14VALVALGLUGLU(CHAIN A AND (RESID 14 THROUGH 46 OR RESID 53...AA14 - 35914 - 359
15VALVALGLUGLU(CHAIN A AND (RESID 14 THROUGH 46 OR RESID 53...AA14 - 35914 - 359
16VALVALGLUGLU(CHAIN A AND (RESID 14 THROUGH 46 OR RESID 53...AA14 - 35914 - 359
17VALVALGLUGLU(CHAIN A AND (RESID 14 THROUGH 46 OR RESID 53...AA14 - 35914 - 359
21VALVALVALVAL(CHAIN B AND (RESID 14 THROUGH 46 OR RESID 53...BB1414
22LYSLYSLYSLYS(CHAIN B AND (RESID 14 THROUGH 46 OR RESID 53...BB5353
23GLUGLUGLUGLU(CHAIN B AND (RESID 14 THROUGH 46 OR RESID 53...BB6666
24VALVALVALVAL(CHAIN B AND (RESID 14 THROUGH 46 OR RESID 53...BB14 - 35414 - 354
25VALVALVALVAL(CHAIN B AND (RESID 14 THROUGH 46 OR RESID 53...BB14 - 35414 - 354
26VALVALVALVAL(CHAIN B AND (RESID 14 THROUGH 46 OR RESID 53...BB14 - 35414 - 354
27VALVALVALVAL(CHAIN B AND (RESID 14 THROUGH 46 OR RESID 53...BB14 - 35414 - 354
31VALVALVALVAL(CHAIN C AND (RESID 14 THROUGH 46 OR RESID 53...CC1414
32LYSLYSLYSLYS(CHAIN C AND (RESID 14 THROUGH 46 OR RESID 53...CC5353
33GLUGLUGLUGLU(CHAIN C AND (RESID 14 THROUGH 46 OR RESID 53...CC6666
34VALVALVALVAL(CHAIN C AND (RESID 14 THROUGH 46 OR RESID 53...CC14 - 35314 - 353
35VALVALVALVAL(CHAIN C AND (RESID 14 THROUGH 46 OR RESID 53...CC14 - 35314 - 353
36VALVALVALVAL(CHAIN C AND (RESID 14 THROUGH 46 OR RESID 53...CC14 - 35314 - 353
37VALVALVALVAL(CHAIN C AND (RESID 14 THROUGH 46 OR RESID 53...CC14 - 35314 - 353
41VALVALVALVAL(CHAIN D AND (RESID 14 THROUGH 46 OR RESID 53...DD1414
42LYSLYSLYSLYS(CHAIN D AND (RESID 14 THROUGH 46 OR RESID 53...DD5353
43GLUGLUGLUGLU(CHAIN D AND (RESID 14 THROUGH 46 OR RESID 53...DD6666
44VALVALVALVAL(CHAIN D AND (RESID 14 THROUGH 46 OR RESID 53...DD14 - 35414 - 354
45VALVALVALVAL(CHAIN D AND (RESID 14 THROUGH 46 OR RESID 53...DD14 - 35414 - 354
46VALVALVALVAL(CHAIN D AND (RESID 14 THROUGH 46 OR RESID 53...DD14 - 35414 - 354
47VALVALVALVAL(CHAIN D AND (RESID 14 THROUGH 46 OR RESID 53...DD14 - 35414 - 354
51VALVALVALVAL(CHAIN E AND (RESID 14 THROUGH 46 OR RESID 53...EE1414
52LYSLYSLYSLYS(CHAIN E AND (RESID 14 THROUGH 46 OR RESID 53...EE5353
53GLUGLUGLUGLU(CHAIN E AND (RESID 14 THROUGH 46 OR RESID 53...EE6666
54VALVALVALVAL(CHAIN E AND (RESID 14 THROUGH 46 OR RESID 53...EE14 - 35414 - 354
55VALVALVALVAL(CHAIN E AND (RESID 14 THROUGH 46 OR RESID 53...EE14 - 35414 - 354
56VALVALVALVAL(CHAIN E AND (RESID 14 THROUGH 46 OR RESID 53...EE14 - 35414 - 354
57VALVALVALVAL(CHAIN E AND (RESID 14 THROUGH 46 OR RESID 53...EE14 - 35414 - 354
61VALVALVALVAL(CHAIN F AND (RESID 14 THROUGH 46 OR RESID 53...FF1414
62LYSLYSLYSLYS(CHAIN F AND (RESID 14 THROUGH 46 OR RESID 53...FF5353
63LYSLYSLYSLYS(CHAIN F AND (RESID 14 THROUGH 46 OR RESID 53...FF105105
64VALVALASPASP(CHAIN F AND (RESID 14 THROUGH 46 OR RESID 53...FF14 - 35514 - 355
65VALVALASPASP(CHAIN F AND (RESID 14 THROUGH 46 OR RESID 53...FF14 - 35514 - 355
66VALVALASPASP(CHAIN F AND (RESID 14 THROUGH 46 OR RESID 53...FF14 - 35514 - 355
67VALVALASPASP(CHAIN F AND (RESID 14 THROUGH 46 OR RESID 53...FF14 - 35514 - 355

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Components

#1: Protein
Magnesium-chelatase subunit ChlI / Mg-protoporphyrin IX chelatase


Mass: 40583.254 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: Kazusa / Gene: chlI, slr1030 / Production host: Escherichia coli (E. coli) / References: UniProt: P51634, magnesium chelatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: sodium malonate, PEG 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 64295 / % possible obs: 98.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.8
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2 / Num. unique obs: 6437

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8P

1g8p


Resolution: 2.91→49.33 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.252 2723 5.14 %
Rwork0.233 50210 -
obs0.234 52933 80.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.61 Å2 / Biso mean: 47.43 Å2 / Biso min: 15.5 Å2
Refinement stepCycle: final / Resolution: 2.91→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12000 0 0 112 12112
Biso mean---37.25 -
Num. residues----1582
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A6694X-RAY DIFFRACTIONPOSITIONAL0
12B6694X-RAY DIFFRACTIONPOSITIONAL0
13C6694X-RAY DIFFRACTIONPOSITIONAL0
14D6694X-RAY DIFFRACTIONPOSITIONAL0
15E6694X-RAY DIFFRACTIONPOSITIONAL0
16F6694X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.91-2.95740.2639810.253135642
2.9574-3.01430.2915840.2415153447
3.0143-3.07580.2564860.2385173453
3.0758-3.14270.25931210.244193959
3.1427-3.21580.29271070.2549210665
3.2158-3.29620.25131240.2513227770
3.2962-3.38530.26691550.2561243075
3.3853-3.48490.29571660.2616251478
3.4849-3.59730.25161550.2457266582
3.5973-3.72590.25871480.2333292989
3.7259-3.8750.24471790.2336309595
3.875-4.05130.25271690.2218320097
4.0513-4.26470.21891650.2104322599
4.2647-4.53180.22821520.2057327599
4.5318-4.88140.24261660.2013322998
4.8814-5.37210.23281730.2271319298
5.3721-6.14820.29132010.2788319498
6.1482-7.74120.24841690.2484318296
7.7412-49.330.24571220.2231313491
Refinement TLS params.Method: refined / Origin x: 96.6474 Å / Origin y: 140.0618 Å / Origin z: 23.3171 Å
111213212223313233
T0.3212 Å20.0043 Å2-0.0035 Å2-0.3446 Å20.0124 Å2--0.271 Å2
L-0.008 °2-0.0531 °20.0094 °2-0.1861 °20.0402 °2---0.1978 °2
S-0.0249 Å °-0.0312 Å °0.0473 Å °0.0305 Å °0.0057 Å °0.0105 Å °-0.0063 Å °0.0057 Å °0.0211 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA14 - 359
2X-RAY DIFFRACTION1ALLA401 - 420
3X-RAY DIFFRACTION1ALLB14 - 354
4X-RAY DIFFRACTION1ALLB401 - 422
5X-RAY DIFFRACTION1ALLC14 - 353
6X-RAY DIFFRACTION1ALLC401 - 419
7X-RAY DIFFRACTION1ALLD14 - 354
8X-RAY DIFFRACTION1ALLD401 - 419
9X-RAY DIFFRACTION1ALLE14 - 354
10X-RAY DIFFRACTION1ALLE401 - 414
11X-RAY DIFFRACTION1ALLF14 - 355
12X-RAY DIFFRACTION1ALLF401 - 418

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