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- PDB-6rnw: The crystal structure of Thermosynechococcus elongatus protochlor... -

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Basic information

Entry
Database: PDB / ID: 6rnw
TitleThe crystal structure of Thermosynechococcus elongatus protochlorophyllide oxidoreductase (POR) in complex with NADP.
ComponentsNADPH-protochlorophyllide oxidoreductase
KeywordsPHOTOSYNTHESIS / Light dependent
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / protochlorophyllide reductase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLevy, C.W.
Funding support United Kingdom, China, 6items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P009042/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/R000093/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M017702/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/J020192/1 United Kingdom
National Science Foundation (China)31230004 China
National Science Foundation (China)2010CB126504 China
CitationJournal: Nature / Year: 2019
Title: Structural basis for enzymatic photocatalysis in chlorophyll biosynthesis.
Authors: Zhang, S. / Heyes, D.J. / Feng, L. / Sun, W. / Johannissen, L.O. / Liu, H. / Levy, C.W. / Li, X. / Yang, J. / Yu, X. / Lin, M. / Hardman, S.J.O. / Hoeven, R. / Sakuma, M. / Hay, S. / Leys, D. ...Authors: Zhang, S. / Heyes, D.J. / Feng, L. / Sun, W. / Johannissen, L.O. / Liu, H. / Levy, C.W. / Li, X. / Yang, J. / Yu, X. / Lin, M. / Hardman, S.J.O. / Hoeven, R. / Sakuma, M. / Hay, S. / Leys, D. / Rao, Z. / Zhou, A. / Cheng, Q. / Scrutton, N.S.
History
DepositionMay 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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 / refine / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH-protochlorophyllide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9822
Polymers39,2381
Non-polymers7431
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-1 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.990, 66.990, 131.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

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Components

#1: Protein NADPH-protochlorophyllide oxidoreductase


Mass: 39238.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Gene: por / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DLC1, protochlorophyllide reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.01 M zinc chloride, 0.1 M sodium acetate pH 5.0, 20 % w/v PEG 6K (A12, PACT screen, Molecular Dimensions Ltd., Newmarket, UK)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.92→43.57 Å / Num. obs: 26888 / % possible obs: 99.96 % / Redundancy: 9.2 % / Biso Wilson estimate: 33.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1265 / Rpim(I) all: 0.044 / Rrim(I) all: 0.1341 / Net I/σ(I): 10.1
Reflection shellResolution: 1.92→1.989 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.588 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 2619 / CC1/2: 0.489 / Rpim(I) all: 0.5652 / Rrim(I) all: 1.687 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RD5

3rd5


Resolution: 1.92→43.57 Å / SU ML: 0.1882 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1374 5.11 %RANDOM
Rwork0.1708 25512 --
obs0.1721 26886 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.62 Å2
Refinement stepCycle: LAST / Resolution: 1.92→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 48 158 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562307
X-RAY DIFFRACTIONf_angle_d0.92623143
X-RAY DIFFRACTIONf_chiral_restr0.0487350
X-RAY DIFFRACTIONf_plane_restr0.0052400
X-RAY DIFFRACTIONf_dihedral_angle_d9.54751853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.990.31791340.26132485X-RAY DIFFRACTION100
1.99-2.070.2671260.23152529X-RAY DIFFRACTION100
2.07-2.160.26321380.20072515X-RAY DIFFRACTION99.96
2.16-2.280.23721410.17912509X-RAY DIFFRACTION100
2.28-2.420.17781340.16012508X-RAY DIFFRACTION100
2.42-2.610.23181250.16712559X-RAY DIFFRACTION100
2.61-2.870.20161380.1712547X-RAY DIFFRACTION100
2.87-3.280.21671440.18132555X-RAY DIFFRACTION100
3.28-4.140.20651550.15072573X-RAY DIFFRACTION99.96
4.14-440.14281390.16182732X-RAY DIFFRACTION99.86

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