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

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Basic information

Entry
Database: PDB / ID: 3aek
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
Protochlorophyllide / 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: 2.3 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 1.2Mar 16, 2016Group: Non-polymer description
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / 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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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

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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)211,0218
Polymers209,0914
Non-polymers1,9294
Water12,845713
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16110 Å2
ΔGint-93 kcal/mol
Surface area57240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.596, 81.219, 175.928
Angle α, β, γ (deg.)90.00, 100.86, 90.00
Int Tables number4
Space group name H-MP1211

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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: 47284.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchN / Plasmid: PBBR1MCS2 / Production host: rhodobacter capsulatus (bacteria) / 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: 57261.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: bchB, bchK / Plasmid: PBBR1MCS2 / Production host: rhodobacter capsulatus (bacteria) / References: UniProt: P26163, EC: 1.18.-.-
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-PMR / Protochlorophyllide / Protochlorophyllide


Mass: 612.957 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H32MgN4O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG4000, 0.2M SODIUM/POTASSIUM PHOSPHATE(PH5.0), pH 8.00, 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: Jun 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 100467 / % possible obs: 99.9 % / Observed criterion σ(I): -2 / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.071

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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: 2.3→34.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.279 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5015 5 %RANDOM
Rwork0.191 ---
obs0.193 95395 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.72 Å2
2--1.25 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12724 0 106 713 13543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02213166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.98817931
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60651669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90723.111540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.317152146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1815108
X-RAY DIFFRACTIONr_chiral_restr0.0870.22062
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029954
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.26441
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.28902
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2826
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3711.58330
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72213385
X-RAY DIFFRACTIONr_scbond_it1.14834960
X-RAY DIFFRACTIONr_scangle_it1.9334.54522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 378 -
Rwork0.236 6872 -
obs--98.45 %
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)
10.8464-0.2751-0.28821.45180.30351.3392-0.0240.1514-0.0835-0.1071-0.06360.05080.1119-0.06450.0876-0.0756-0.05570.0429-0.0969-0.0161-0.178256.141436.9007100.7611
21.2593-0.1252-0.67930.81850.06391.63510.0453-0.17830.1845-0.06660.0241-0.0719-0.22660.2625-0.0695-0.1298-0.0947-0.0204-0.0939-0.0387-0.087958.039361.6206128.0195
31.16850.4041-0.13171.2642-0.42271.42380.0281-0.2911-0.09430.0278-0.0713-0.02260.08930.00060.0432-0.15590.03230.0392-0.035-0.0092-0.14117.087541.733158.3245
41.61120.249-0.87970.73540.16771.76270.06280.18930.3319-0.0858-0.00770.1508-0.2482-0.3148-0.0551-0.11430.0988-0.061-0.08260.0309-0.010118.261464.2936129.2275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 421
2X-RAY DIFFRACTION2B1 - 418
3X-RAY DIFFRACTION3C7 - 420
4X-RAY DIFFRACTION4D1 - 418

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