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- PDB-6l1h: Crystal structure of light-dependent protochlorophyllide oxidored... -

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Basic information

Entry
Database: PDB / ID: 6l1h
TitleCrystal structure of light-dependent protochlorophyllide oxidoreductase from Thermosynechococcus elongatus
ComponentsNADPH-protochlorophyllide oxidoreductase
KeywordsOXIDOREDUCTASE / chlorophyll biosynthesis / photocatalysis / NADPH
Function / homology
Function and homology information


protochlorophyllide reductase / protochlorophyllide reductase activity / chlorophyll biosynthetic process / photosynthesis / nucleotide binding / metal ion binding
Similarity search - Function
Light-dependent protochlorophyllide reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Protochlorophyllide reductase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.409 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH-protochlorophyllide oxidoreductase
B: NADPH-protochlorophyllide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4384
Polymers73,9472
Non-polymers1,4912
Water3,315184
1
A: NADPH-protochlorophyllide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7192
Polymers36,9741
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-4 kcal/mol
Surface area12850 Å2
MethodPISA
2
B: NADPH-protochlorophyllide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7192
Polymers36,9741
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-4 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.899, 96.200, 141.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 70 or resid 72...
21(chain B and (resid 5 through 27 or (resid 28...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 70 or resid 72...A5 - 70
121(chain A and (resid 5 through 70 or resid 72...A72 - 74
131(chain A and (resid 5 through 70 or resid 72...A5 - 400
141(chain A and (resid 5 through 70 or resid 72...A94 - 1
151(chain A and (resid 5 through 70 or resid 72...A2
161(chain A and (resid 5 through 70 or resid 72...A5 - 400
171(chain A and (resid 5 through 70 or resid 72...A5 - 400
181(chain A and (resid 5 through 70 or resid 72...A5 - 400
191(chain A and (resid 5 through 70 or resid 72...A5 - 400
211(chain B and (resid 5 through 27 or (resid 28...B5 - 27
221(chain B and (resid 5 through 27 or (resid 28...B28
231(chain B and (resid 5 through 27 or (resid 28...B5 - 400
241(chain B and (resid 5 through 27 or (resid 28...B5 - 400
251(chain B and (resid 5 through 27 or (resid 28...B5 - 400
261(chain B and (resid 5 through 27 or (resid 28...B5 - 400

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Components

#1: Protein NADPH-protochlorophyllide oxidoreductase / light-dependent protochlorophyllide oxidoreductas


Mass: 36973.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: por / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DLC1, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 20% (w/v) PEG 4,000, 10% (w/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27727 / % possible obs: 96.9 % / Redundancy: 11 % / Biso Wilson estimate: 42.97 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.036 / Net I/σ(I): 18.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.547 / Num. unique obs: 2401 / CC1/2: 0.913 / Rpim(I) all: 0.183 / % possible all: 85.6

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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: 2.409→49.56 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1329 4.8 %
Rwork0.1808 26350 -
obs0.1827 27679 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.9 Å2 / Biso mean: 39.6707 Å2 / Biso min: 23.66 Å2
Refinement stepCycle: final / Resolution: 2.409→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4709 0 96 184 4989
Biso mean--33.04 40.77 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044947
X-RAY DIFFRACTIONf_angle_d0.7836718
X-RAY DIFFRACTIONf_chiral_restr0.05749
X-RAY DIFFRACTIONf_plane_restr0.005845
X-RAY DIFFRACTIONf_dihedral_angle_d15.422940
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2658X-RAY DIFFRACTION11.191TORSIONAL
12B2658X-RAY DIFFRACTION11.191TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.409-2.5050.29691350.2429239381
2.505-2.6190.28281470.2089292998
2.619-2.75710.2491530.20412999100
2.7571-2.92980.26711410.20272992100
2.9298-3.1560.22811470.1996300199
3.156-3.47350.2451510.1948294398
3.4735-3.9760.22641390.1772302799
3.976-5.00860.18091460.1504290994
5.0086-49.560.19661700.1692315798

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