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- PDB-3aet: Structure of the light-independent protochlorophyllide reductase ... -

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Basic information

Entry
Database: PDB / ID: 3aet
TitleStructure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark
Components
  • Light-independent protochlorophyllide reductase subunit B
  • Light-independent protochlorophyllide reductase subunit N
KeywordsOXIDOREDUCTASE / Iron/sulfur cluster / Bacteriochlorophyll biosynthesis / Chlorophyll biosynthesis / Photosynthesis
Function / homology
Function and homology information


ferredoxin:protochlorophyllide reductase (ATP-dependent) / photosynthesis, dark reaction / light-independent bacteriochlorophyll biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / oxidoreductase activity, acting on iron-sulfur proteins as donors / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 - #20 / Light-independent protochlorophyllide reductase, N subunit / Light-independent protochlorophyllide reductase, B subunit / Protochlorophyllide reductase, ChlB, light independent / Light-independent protochlorophyllide reductase subunit B-like, C-terminal / Proto-chlorophyllide reductase, C-terminal / Proto-chlorophyllide reductase 57 kD subunit / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase ...Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 - #20 / Light-independent protochlorophyllide reductase, N subunit / Light-independent protochlorophyllide reductase, B subunit / Protochlorophyllide reductase, ChlB, light independent / Light-independent protochlorophyllide reductase subunit B-like, C-terminal / Proto-chlorophyllide reductase, C-terminal / Proto-chlorophyllide reductase 57 kD subunit / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase / Nitrogenase molybdenum iron protein domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Light-independent protochlorophyllide reductase subunit B / Light-independent protochlorophyllide reductase subunit N
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsMuraki, N. / Nomata, J. / Shiba, T. / Fujita, Y. / Kurisu, G.
CitationJournal: Nature / Year: 2010
Title: X-ray crystal structure of the light-independent protochlorophyllide reductase
Authors: Muraki, N. / Nomata, J. / Ebata, K. / Mizoguchi, T. / Shiba, T. / Tamiaki, H. / Kurisu, G. / Fujita, Y.
History
DepositionFeb 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
A: Light-independent protochlorophyllide reductase subunit N
B: Light-independent protochlorophyllide reductase subunit B
C: Light-independent protochlorophyllide reductase subunit N
D: Light-independent protochlorophyllide reductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,6276
Polymers208,9234
Non-polymers7032
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-91 kcal/mol
Surface area58080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.442, 81.440, 95.864
Angle α, β, γ (deg.)102.53, 110.89, 94.44
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13A
23C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALA3AA7 - 8019 - 92
21THRTHRALAALA3CC7 - 8019 - 92
12METMETGLUGLU3BB1 - 4201 - 420
22METMETGLUGLU3DD1 - 4201 - 420
13ASPASPGLYGLY4AA90 - 421102 - 433
23ASPASPASNASN4CC90 - 420102 - 432

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Light-independent protochlorophyllide reductase subunit N / LI-POR subunit N / DPOR subunit N / dark-operative protochlorophyllide oxidoreductase N-protein


Mass: 47212.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchN / Plasmid: PASK-IBA5PLUS / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P26164, EC: 1.18.-.-
#2: Protein Light-independent protochlorophyllide reductase subunit B / LI-POR subunit B / DPOR subunit B / dark-operative protochlorophyllide oxidoreductase B-protein


Mass: 57249.590 Da / Num. of mol.: 2 / Mutation: D36C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchB, bchK / Plasmid: PASK-IBA5PLUS / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P26163, EC: 1.18.-.-
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.2M SODIUM CLORIDE, 0.1M MOPS-NAOH(PH7.0), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 42863 / Observed criterion σ(I): -2 / Biso Wilson estimate: 69.55 Å2 / Rmerge(I) obs: 0.093

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZMP

2zmp
PDB Unreleased entry


Resolution: 2.91→40.05 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.873 / SU B: 42.917 / SU ML: 0.371 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2171 5.1 %RANDOM
Rwork0.211 ---
obs0.215 40688 89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å21 Å2-0.63 Å2
2---2.41 Å2-0.87 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.91→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12760 0 16 6 12782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213052
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9817759
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94751665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48623.086538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.76152146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.93415108
X-RAY DIFFRACTIONr_chiral_restr0.1010.22060
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029826
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.26629
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.28950
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2454
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4191.58501
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.765213373
X-RAY DIFFRACTIONr_scbond_it1.07235003
X-RAY DIFFRACTIONr_scangle_it1.8444.54362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A296tight positional0.060.05
2B1680tight positional0.040.05
3A2531medium positional0.360.5
1A275loose positional0.575
2B1538loose positional0.515
1A296tight thermal0.10.5
2B1680tight thermal0.110.5
3A2531medium thermal0.282
1A275loose thermal0.810
2B1538loose thermal0.8710
LS refinement shellResolution: 2.91→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 92 -
Rwork0.379 1732 -
obs--51.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16370.14410.54630.773-0.03551.32690.06860.1083-0.04-0.3405-0.05810.01990.27360.0095-0.01050.18220.04030.0309-0.0915-0.0759-0.178-12.6769-19.5008-28.7768
20.6670.04870.02821.2240.35181.71640.00170.0911-0.07230.0534-0.1754-0.27660.41460.20860.1737-0.06220.1270.0544-0.09470.090.010411.1162-19.7841-1.0198
30.9321-0.0842-0.53350.7448-0.21211.330.0105-0.06930.0170.3492-0.07330.0596-0.2133-0.05170.06290.1693-0.0381-0.0561-0.1493-0.0599-0.1847-12.957419.456328.7532
40.434-0.13570.08241.32930.23651.5914-0.04110.07110.0981-0.0647-0.186-0.3081-0.28660.19150.2271-0.1157-0.1372-0.0375-0.11920.12660.048510.736820.00870.9257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 421
2X-RAY DIFFRACTION2B1 - 420
3X-RAY DIFFRACTION3C7 - 420
4X-RAY DIFFRACTION4D1 - 420

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