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- PDB-6l1g: Crystal structure of light-dependent protochlorophyllide oxidored... -

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Basic information

Entry
Database: PDB / ID: 6l1g
TitleCrystal structure of light-dependent protochlorophyllide oxidoreductase from Synechocystis sp. PCC 6803
ComponentsLight-dependent protochlorophyllide reductase
KeywordsOXIDOREDUCTASE / chlorophyll biosynthesis / photocatalysis / NADPH
Function / homology
Function and homology information


protochlorophyllide reductase / protochlorophyllide reductase activity / chlorophyll biosynthetic process / photosynthesis
Similarity search - Function
Light-dependent protochlorophyllide reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / Light-dependent protochlorophyllide reductase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsDong, C. / Wang, X. / Liu, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase.
Authors: Dong, C.S. / Zhang, W.L. / Wang, Q. / Li, Y.S. / Wang, X. / Zhang, M. / Liu, L.
History
DepositionSep 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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: Light-dependent protochlorophyllide reductase
B: Light-dependent protochlorophyllide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4378
Polymers76,5622
Non-polymers1,8756
Water3,801211
1
A: Light-dependent protochlorophyllide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2184
Polymers38,2811
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area13210 Å2
MethodPISA
2
B: Light-dependent protochlorophyllide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2184
Polymers38,2811
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-25 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.010, 57.122, 72.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 5 and (name N or name...
21(chain B and (resid 5 through 48 or (resid 49...

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
11METMETMETMET(chain A and ((resid 5 and (name N or name...AA525
12METMETNDPNDP(chain A and ((resid 5 and (name N or name...AA - C5 - 40025
13METMETNDPNDP(chain A and ((resid 5 and (name N or name...AA - C5 - 40025
14METMETNDPNDP(chain A and ((resid 5 and (name N or name...AA - C5 - 40025
15METMETNDPNDP(chain A and ((resid 5 and (name N or name...AA - C5 - 40025
21METMETASPASP(chain B and (resid 5 through 48 or (resid 49...BB5 - 4825 - 68
22GLUGLUGLUGLU(chain B and (resid 5 through 48 or (resid 49...BB4969
23PROPROLEULEU(chain B and (resid 5 through 48 or (resid 49...BB4 - 32124 - 341
24PROPROLEULEU(chain B and (resid 5 through 48 or (resid 49...BB4 - 32124 - 341
25PROPROLEULEU(chain B and (resid 5 through 48 or (resid 49...BB4 - 32124 - 341

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Components

#1: Protein Light-dependent protochlorophyllide reductase / PCR / NADPH-protochlorophyllide oxidoreductase / POR


Mass: 38280.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: por, pcr, slr0506 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59987, protochlorophyllide reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 1.5 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 33980 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 37.22 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.052 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.9 % / Num. unique obs: 3338 / CC1/2: 0.686 / Rpim(I) all: 0.428 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RD5

3rd5


Resolution: 2.2→46.086 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 1710 5.06 %
Rwork0.1786 32085 -
obs0.1801 33795 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.17 Å2 / Biso mean: 43.8217 Å2 / Biso min: 22.55 Å2
Refinement stepCycle: final / Resolution: 2.2→46.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4615 0 116 211 4942
Biso mean--38.62 50.58 -
Num. residues----594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044847
X-RAY DIFFRACTIONf_angle_d0.7276579
X-RAY DIFFRACTIONf_chiral_restr0.046730
X-RAY DIFFRACTIONf_plane_restr0.005817
X-RAY DIFFRACTIONf_dihedral_angle_d11.3362833
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2632X-RAY DIFFRACTION10.983TORSIONAL
12B2632X-RAY DIFFRACTION10.983TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.26480.28141440.2573257799
2.2648-2.33790.30041490.22422605100
2.3379-2.42140.23671360.21832660100
2.4214-2.51840.26091350.21012652100
2.5184-2.6330.26391370.19722643100
2.633-2.77180.22641590.20482618100
2.7718-2.94540.25251250.19062680100
2.9454-3.17280.23731430.18762686100
3.1728-3.4920.21221370.18242667100
3.492-3.9970.18791390.15412703100
3.997-5.03480.1731500.13732740100
5.0348-46.0860.16791560.16782854100
Refinement TLS params.Method: refined / Origin x: 57.4107 Å / Origin y: 29.3437 Å / Origin z: 12.0655 Å
111213212223313233
T0.1986 Å2-0.0063 Å20.0044 Å2-0.262 Å2-0.0226 Å2--0.2905 Å2
L0.1602 °2-0.2749 °20.3631 °2-1.2434 °2-1.3434 °2--2.15 °2
S-0.0322 Å °-0.0224 Å °-0.0059 Å °-0.0008 Å °0.0098 Å °-0.0105 Å °0.0466 Å °0.0016 Å °0.0309 Å °
Refinement TLS groupSelection details: all

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