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- PDB-1lqt: A covalent modification of NADP+ revealed by the atomic resolutio... -

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Basic information

Entry
Database: PDB / ID: 1lqt
TitleA covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase
ComponentsFprA
KeywordsOXIDOREDUCTASE / NADP+ derivative / tuberculosis / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


ferredoxin-NAD+ reductase activity / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADP+ binding / peptidoglycan-based cell wall / flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
Ferredoxin-NADP+ reductase, adrenodoxin-type / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / Rossmann fold ...Ferredoxin-NADP+ reductase, adrenodoxin-type / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / 4-OXO-NICOTINAMIDE-ADENINE DINUCLEOTIDE PHOSPHATE / NADPH-ferredoxin reductase FprA / NADPH-ferredoxin reductase FprA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBossi, R.T. / Aliverti, A. / Raimondi, D. / Fischer, F. / Zanetti, G. / Ferrari, D. / Tahallah, N. / Maier, C.S. / Heck, A.J.R. / Rizzi, M. ...Bossi, R.T. / Aliverti, A. / Raimondi, D. / Fischer, F. / Zanetti, G. / Ferrari, D. / Tahallah, N. / Maier, C.S. / Heck, A.J.R. / Rizzi, M. / Mattevi, A. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Biochemistry / Year: 2002
Title: A covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase.
Authors: Bossi, R.T. / Aliverti, A. / Raimondi, D. / Fischer, F. / Zanetti, G. / Ferrari, D. / Tahallah, N. / Maier, C.S. / Heck, A.J.R. / Rizzi, M. / Mattevi, A.
History
DepositionMay 13, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / pdbx_distant_solvent_atoms ...database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FprA
B: FprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,54917
Polymers98,8082
Non-polymers3,74115
Water33,5801864
1
A: FprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2458
Polymers49,4041
Non-polymers1,8417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3049
Polymers49,4041
Non-polymers1,9008
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.335, 89.215, 160.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FprA / ferredoxin NADP reductase


Mass: 49403.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O05783, UniProt: P9WIQ3*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-ODP / 4-OXO-NICOTINAMIDE-ADENINE DINUCLEOTIDE PHOSPHATE


Type: RNA linking / Mass: 760.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O18P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1864 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
210 mMHEPES-KOH1droppH7.0
310 %(v/v)glycerol1drop
45 mMdithiothreitol1drop
50.65 mMNADP+1drop
630 %(w/v)PEG40001reservoir
70.1 Msodium citrate1reservoirpH5.6
80.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 31, 2001
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→20 Å / Num. all: 440216 / Num. obs: 440216 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 5.1
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 62782 / Rsym value: 0.485 / % possible all: 93.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 1170509
Reflection shell
*PLUS
% possible obs: 95.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
BEASTmodel building
REFMAC5refinement
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E1L

1e1l


Resolution: 1.05→40 Å / Cor.coef. Fo:Fc: 0.983 / SU B: 0.756 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 2200 -RANDOM
Rwork0.13393 ---
all0.1339 440131 --
obs0.13393 440131 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6908 0 248 1864 9020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0217499
X-RAY DIFFRACTIONr_bond_other_d0.0010.026929
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.99810336
X-RAY DIFFRACTIONr_angle_other_deg0.918316156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0863967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.938151304
X-RAY DIFFRACTIONr_chiral_restr0.1570.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028385
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021447
X-RAY DIFFRACTIONr_nbd_refined0.3950.31853
X-RAY DIFFRACTIONr_nbd_other0.2130.37460
X-RAY DIFFRACTIONr_nbtor_other0.9870.56
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.51497
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3070.59
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4260.322
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.395
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3020.5129
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0940.51
X-RAY DIFFRACTIONr_mcbond_it1.4681.54661
X-RAY DIFFRACTIONr_mcangle_it2.17227594
X-RAY DIFFRACTIONr_scbond_it332838
X-RAY DIFFRACTIONr_scangle_it4.4984.52737
X-RAY DIFFRACTIONr_rigid_bond_restr1.38227499
X-RAY DIFFRACTIONr_sphericity_free10.89551881
X-RAY DIFFRACTIONr_sphericity_bonded4.94757344
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.324 184
Rwork0.3 31536
obs-31536
Refinement
*PLUS
% reflection Rfree: 0.5 % / Rfactor Rwork: 0.134
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.747

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