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- PDB-2xdq: Dark Operative Protochlorophyllide Oxidoreductase (ChlN-ChlB)2 Complex -

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Basic information

Entry
Database: PDB / ID: 2xdq
TitleDark Operative Protochlorophyllide Oxidoreductase (ChlN-ChlB)2 Complex
Components(LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT ...) x 2
KeywordsOXIDOREDUCTASE / DPOR / (BACTERIO)CHLOROPHYLL BIOSYNTHESIS / PHOTOSYNTHESIS / NITROGENASE-LIKE
Function / homology
Function and homology information


light-independent chlorophyll biosynthetic process / ferredoxin:protochlorophyllide reductase (ATP-dependent) / photosynthesis, dark reaction / 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
1-METHYLGUANIDINE / IRON/SULFUR CLUSTER / Light-independent protochlorophyllide reductase subunit B / Light-independent protochlorophyllide reductase subunit N
Similarity search - Component
Biological speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsBroecker, M.J. / Schomburg, S. / Heinz, D.W. / Jahn, D. / Schubert, W.-D. / Moser, J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal Structure of the Nitrogenase-Like Dark Operative Protochlorophyllide Oxidoreductase Catalytic Complex (Chln/Chlb)2.
Authors: Broecker, M.J. / Schomburg, S. / Heinz, D.W. / Jahn, D. / Schubert, W.-D. / Moser, J.
History
DepositionMay 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Data collection / Version format compliance
Revision 1.2Apr 19, 2017Group: Data collection
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7776
Polymers108,1602
Non-polymers6174
Water2,522140
1
A: LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N
B: LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B
hetero molecules

A: LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N
B: LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,55312
Polymers216,3194
Non-polymers1,2348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area19280 Å2
ΔGint-137.7 kcal/mol
Surface area60050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.095, 192.095, 132.504
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT ... , 2 types, 2 molecules AB

#1: Protein LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N / LI-POR SUBUNIT N / DPOR SUBUNIT N / CHLN


Mass: 51562.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DGH2, EC: 1.18.-.-
#2: Protein LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B / LI-POR SUBUNIT B / DPOR SUBUNIT B / CHLB


Mass: 56597.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DGC6, EC: 1.18.-.-

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Non-polymers , 4 types, 144 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-MGX / 1-METHYLGUANIDINE


Mass: 73.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7N3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.31 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: PROTEIN CONCENTRATION = 10 MG/ML TEMPERATURE = 17 DEGREES C ATMOSPHERE - ANAEROBIC, REDUCING METHOD - HANGING DROP VOLUMES - 3MICROL PROTEIN - 3MICROL RESERVOIR SOLUTION RESERVOIR - 9.5% PEG ...Details: PROTEIN CONCENTRATION = 10 MG/ML TEMPERATURE = 17 DEGREES C ATMOSPHERE - ANAEROBIC, REDUCING METHOD - HANGING DROP VOLUMES - 3MICROL PROTEIN - 3MICROL RESERVOIR SOLUTION RESERVOIR - 9.5% PEG 6000, 85MM HEPES PH 7.1, CRYOPROTECTANT - 14% MPD, 15% GLYCEROL

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID2910.91
SYNCHROTRONSOLEIL PROXIMA 120.9790, 0.9795
Detector
TypeIDDetectorDate
ADSC CCD1CCDDec 10, 2007
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.911
20.9791
30.97951
ReflectionResolution: 2.4→25 Å / Num. obs: 54878 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 8.3 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXC D Ephasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.4→103.65 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 19.213 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 2817 5.1 %RANDOM
Rwork0.20127 ---
obs0.20408 52744 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.175 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å21.41 Å20 Å2
2--2.82 Å20 Å2
3----4.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→103.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6793 0 23 140 6956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227138
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9669760
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3365903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55523.343332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.666151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0221562
X-RAY DIFFRACTIONr_chiral_restr0.1160.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215426
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4481.52146
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83423481
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.13331346
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8924.51260
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 219 -
Rwork0.337 3812 -
obs--98.34 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6890.89620.28671.5168-0.39293.35780.0603-0.48510.31120.01970.08570.2705-0.3525-0.5197-0.1460.23550.3383-0.08490.6694-0.17260.45039.23793.09776.398
21.34950.73910.15650.4527-0.18043.0214-0.02710.1235-0.13950.01010.2117-0.10040.1998-0.5004-0.18460.16450.1678-0.1420.5499-0.07320.366510.88175.9948.953
33.91380.4099-2.52631.69611.93175.3728-0.0194-0.0534-0.15410.37240.0778-0.04760.7733-0.6828-0.05840.3308-0.1157-0.2030.94540.09150.3087-2.6670.06967.477
42.24290.81021.761.16530.48625.56650.0065-0.4495-0.13660.14660.17060.18680.5254-1.1158-0.17710.2158-0.0028-0.02240.96190.07530.307-4.68675.76980.737
510.72993.84721.40211.38520.44431.1180.4087-0.3777-0.25790.1449-0.1305-0.07810.0891-0.2041-0.27820.1130.1441-0.08010.336-0.03970.188517.88282.18983.084
64.8760.67480.16443.7859-0.64240.1265-0.14-0.36090.3826-1.06520.24330.70840.1742-0.0556-0.10320.676-0.0015-0.06340.4959-0.07650.402932.877100.85879.056
70.93140.5632-0.18391.88290.02341.2437-0.0418-0.05970.1761-0.11330.09450.3331-0.3195-0.3051-0.05260.36310.353-0.10520.3902-0.07120.422920.16998.66650.969
81.6691-0.67730.71471.0753-0.95411.02660.0299-0.10470.1904-0.0422-0.0365-0.0057-0.17480.05930.00660.4970.1698-0.00680.229-0.06970.279943.243102.49647.607
91.7553-0.33991.15197.4431-3.96422.72610.06470.10280.0728-0.1905-0.3642-0.45690.12130.38150.29960.26420.12960.15510.45450.03450.245361.89890.35250.004
102.2388-0.05530.40030.9846-0.69671.78610.0494-0.1295-0.1961-0.3415-0.0990.03760.04120.02590.04950.38030.2475-0.04060.275-0.02250.282742.3373.16147.944
111.0085-1.07260.55873.44040.37461.22630.0223-0.2944-0.2534-0.09210.0590.30770.0935-0.0236-0.08140.23430.2207-0.00720.40870.07930.263646.81273.16262.118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 18
2X-RAY DIFFRACTION1A309 - 425
3X-RAY DIFFRACTION2A19 - 144
4X-RAY DIFFRACTION2A602
5X-RAY DIFFRACTION3A145 - 259
6X-RAY DIFFRACTION4A260 - 308
7X-RAY DIFFRACTION5A426 - 450
8X-RAY DIFFRACTION6A486 - 494
9X-RAY DIFFRACTION7B-2 - 129
10X-RAY DIFFRACTION8B130 - 248
11X-RAY DIFFRACTION9B249 - 291
12X-RAY DIFFRACTION10B292 - 398
13X-RAY DIFFRACTION11B399 - 443

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