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

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Basic information

Entry
Database: PDB / ID: 6rnv
TitleThe crystal structure of Thermosynechococcus elongatus protochlorophyllide oxidoreductase (POR)
ComponentsThermosynechococcus elongatus protochlorophyllide oxidoreductase (POR)
KeywordsPHOTOSYNTHESIS / Light dependent
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
Protochlorophyllide reductase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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: Thermosynechococcus elongatus protochlorophyllide oxidoreductase (POR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0453
Polymers36,9741
Non-polymers712
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.847, 66.847, 133.008
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-635-

HOH

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Components

#1: Protein Thermosynechococcus elongatus protochlorophyllide oxidoreductase (POR)


Mass: 36973.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8DLC1*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.88 Å3/Da / Density % sol: 57.29 %
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
Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.27→53.08 Å / Num. obs: 91463 / % possible obs: 98.76 % / Redundancy: 17.5 % / Biso Wilson estimate: 14.04 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.0928 / Rpim(I) all: 0.02207 / Rrim(I) all: 0.09546 / Net I/σ(I): 14.73
Reflection shellResolution: 1.27→1.315 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.8746 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 9068 / CC1/2: 0.541 / Rpim(I) all: 0.2592 / Rrim(I) all: 0.9132 / % possible all: 96.46

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Processing

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

3rd5


Resolution: 1.27→53.08 Å / SU ML: 0.157 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.7851
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 4593 5.08 %Random
Rwork0.1528 ---
obs0.1544 90346 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.19 Å2
Refinement stepCycle: LAST / Resolution: 1.27→53.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 2 363 2455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982378
X-RAY DIFFRACTIONf_angle_d1.173246
X-RAY DIFFRACTIONf_chiral_restr0.1928353
X-RAY DIFFRACTIONf_plane_restr0.0081429
X-RAY DIFFRACTIONf_dihedral_angle_d4.8371793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.36511830.34882731X-RAY DIFFRACTION95.73
1.28-1.30.32421540.32942718X-RAY DIFFRACTION96.38
1.3-1.320.34481690.30842772X-RAY DIFFRACTION96.9
1.32-1.330.36151550.30342766X-RAY DIFFRACTION97.2
1.33-1.350.29661370.27732779X-RAY DIFFRACTION97.17
1.35-1.370.29891450.26912825X-RAY DIFFRACTION97.99
1.37-1.390.29491820.25272759X-RAY DIFFRACTION97.64
1.39-1.410.24721650.232758X-RAY DIFFRACTION97.66
1.41-1.430.26821350.21462840X-RAY DIFFRACTION97.96
1.43-1.450.24511500.20472809X-RAY DIFFRACTION98.18
1.45-1.480.25531740.18312808X-RAY DIFFRACTION98.42
1.48-1.510.19141380.16272839X-RAY DIFFRACTION98.67
1.51-1.530.1871650.15192826X-RAY DIFFRACTION98.88
1.53-1.570.18961550.14132833X-RAY DIFFRACTION98.97
1.57-1.60.19391380.1352868X-RAY DIFFRACTION99.08
1.6-1.640.16911480.13232878X-RAY DIFFRACTION99.25
1.64-1.680.15051720.12022842X-RAY DIFFRACTION99.44
1.68-1.720.14971540.12282845X-RAY DIFFRACTION99.5
1.72-1.770.14451450.11982879X-RAY DIFFRACTION99.57
1.77-1.830.16291620.11782858X-RAY DIFFRACTION99.41
1.83-1.90.14321070.11892942X-RAY DIFFRACTION99.64
1.9-1.970.14291400.12572904X-RAY DIFFRACTION99.77
1.97-2.060.16571400.12392893X-RAY DIFFRACTION99.57
2.06-2.170.16381440.12862927X-RAY DIFFRACTION99.84
2.17-2.310.16091480.12282924X-RAY DIFFRACTION99.87
2.31-2.490.14041460.13042930X-RAY DIFFRACTION99.81
2.49-2.740.16191750.13762899X-RAY DIFFRACTION99.87
2.74-3.130.17251460.14862963X-RAY DIFFRACTION99.9
3.13-3.950.1771810.14682986X-RAY DIFFRACTION100
3.95-57.950.21051400.16593152X-RAY DIFFRACTION99.76

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