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- PDB-6r46: Crystal structure of LPOR (Thermosynechococcus elongatus) complex... -

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Basic information

Entry
Database: PDB / ID: 6r46
TitleCrystal structure of LPOR (Thermosynechococcus elongatus) complexed with NADP+ at 2.5A resolution
ComponentsNADPH-protochlorophyllide oxidoreductase
KeywordsHYDROLASE / complex
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 domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Protochlorophyllide reductase
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhou, A. / Feng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) 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
DepositionMar 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-protochlorophyllide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,02511
Polymers35,8121
Non-polymers1,21210
Water36020
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-156 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.950, 134.950, 104.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-407-

CL

21A-409-

CL

31A-520-

HOH

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Components

#1: Protein NADPH-protochlorophyllide oxidoreductase


Mass: 35812.340 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Gene: por / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DLC1, protochlorophyllide reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 10MM ZNSO4,0.2M LI3CITRATE, 30% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.5→78 Å / Num. obs: 20005 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 20005 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0189refinement
RefinementMethod to determine structure: SAD / Resolution: 2.5→78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.784 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.216 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 976 4.9 %RANDOM
Rwork0.196 ---
obs0.198 19000 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 57 20 2217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192236
X-RAY DIFFRACTIONr_bond_other_d0.0020.022104
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9923032
X-RAY DIFFRACTIONr_angle_other_deg1.00134871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21223.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6315375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8151515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3575.1941096
X-RAY DIFFRACTIONr_mcbond_other2.3485.1921095
X-RAY DIFFRACTIONr_mcangle_it3.7487.7661363
X-RAY DIFFRACTIONr_mcangle_other3.7487.7671364
X-RAY DIFFRACTIONr_scbond_it2.9125.8491140
X-RAY DIFFRACTIONr_scbond_other2.9115.8571141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7788.7141670
X-RAY DIFFRACTIONr_long_range_B_refined8.30761.5132412
X-RAY DIFFRACTIONr_long_range_B_other8.30861.532412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 66 -
Rwork0.288 1358 -
obs--99.23 %
Refinement TLS params.Method: refined / Origin x: -40.8526 Å / Origin y: -33.9259 Å / Origin z: -9.5193 Å
111213212223313233
T0.1973 Å2-0.0375 Å2-0.0155 Å2-0.1759 Å20.0717 Å2--0.0654 Å2
L0.3868 °20.2329 °20.3143 °2-0.9418 °2-0.0484 °2--0.8905 °2
S-0.1127 Å °0.0942 Å °0.1173 Å °0.2315 Å °-0.1068 Å °0.0185 Å °-0.0206 Å °0.1758 Å °0.2195 Å °

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