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- PDB-2kru: Solution NMR structure of the PCP_red domain of light-independent... -

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Basic information

Entry
Database: PDB / ID: 2kru
TitleSolution NMR structure of the PCP_red domain of light-independent protochlorophyllide reductase subunit B from Chlorobium tepidum. Northeast Structural Genomics Consortium Target CtR69A
ComponentsLight-independent protochlorophyllide reductase subunit B
KeywordsOXIDOREDUCTASE / NESG / PSI / bchB / Bacteriochlorophyll biosynthesis / Chlorophyll biosynthesis / Photosynthesis / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
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
Proto-chlorophyllide reductase 57 kD subunit B / 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/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Light-independent protochlorophyllide reductase subunit B
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHe, Y. / Eletsky, A. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the PCP_red domain of light-independent protochlorophyllide reductase subunit B from Chlorobium tepidum. Northeast Structural Genomics Consortium Target CtR69A
Authors: He, Y. / Eletsky, A. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionDec 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Structure summary
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light-independent protochlorophyllide reductase subunit B


Theoretical massNumber of molelcules
Total (without water)7,3191
Polymers7,3191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Light-independent protochlorophyllide reductase subunit B / LI-POR subunit B / DPOR subunit B


Mass: 7319.390 Da / Num. of mol.: 1 / Fragment: residues 484-537
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Strain: TLS / Gene: bchB, CT2151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9F715, EC: 1.18.-.-

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C CT-HSQC ali
1322D 1H-13C CT-HSQC (methyl)
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY ali
110113C/15N-NOESY
11112D 1H-13C CT-HSQC aro
11213D (H)CCH-COSY aro
11312D 1H-15N LR-HSQC (Histidine)

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Sample preparation

Details
Solution-IDContentsSolvent system
11.080 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
20.986 mM [U-5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.080 mMprotein[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMsodium chloride1
5 mMcalcium chloride1
0.02 %NaN31
0.986 mMprotein[U-5% 13C; U-100% 15N]2
20 mMMES2
100 mMsodium chloride2
5 mMcalcium chloride2
0.02 %NaN32
Sample conditionsIonic strength: 117.5 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.4Guntertprocessing
XEASYBartels et al.data analysis
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxdata analysis
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichdata analysis
PSVS1.3Bhattacharya and Montelionevalidation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA v2.1 using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the ...Details: Structure determination was performed iteratively with CYANA v2.1 using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with OPLSX force field.
NMR constraintsNOE constraints total: 1013 / NOE intraresidue total count: 219 / NOE long range total count: 262 / NOE medium range total count: 273 / NOE sequential total count: 259 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 35 / Protein psi angle constraints total count: 35
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.06 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.5 ° / Maximum upper distance constraint violation: 0.224 Å
NMR ensemble rmsDistance rms dev: 0.011 Å

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