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- PDB-4dqv: Crystal structure of reductase (R) domain of non-ribosomal peptid... -

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Basic information

Entry
Database: PDB / ID: 4dqv
TitleCrystal structure of reductase (R) domain of non-ribosomal peptide synthetase from Mycobacterium tuberculosis
ComponentsPROBABLE PEPTIDE SYNTHETASE NRP (PEPTIDE SYNTHASE)
KeywordsLIGASE / GxxGxxG motif / Rossmann fold / Short chain Dehydrogenase/Reductase family / Reductase / lipopeptide
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / ligase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / transferase activity / ATP binding ...amino acid activation for nonribosomal peptide biosynthetic process / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / ligase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / transferase activity / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site ...Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isonitrile lipopeptide synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHaque, A.S. / Panjikar, S. / Sankaranarayanan, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Nonprocessive [2 + 2]e- off-loading reductase domains from mycobacterial nonribosomal peptide synthetases.
Authors: Chhabra, A. / Haque, A.S. / Pal, R.K. / Goyal, A. / Rai, R. / Joshi, S. / Panjikar, S. / Pasha, S. / Sankaranarayanan, R. / Gokhale, R.S.
History
DepositionFeb 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE PEPTIDE SYNTHETASE NRP (PEPTIDE SYNTHASE)


Theoretical massNumber of molelcules
Total (without water)52,7261
Polymers52,7261
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.058, 59.058, 238.988
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROBABLE PEPTIDE SYNTHETASE NRP (PEPTIDE SYNTHASE)


Mass: 52725.949 Da / Num. of mol.: 1 / Fragment: Reductase domain, UNP RESIDUES 2056-2512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: nrp, Rv0101, rv101 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10896, Ligases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.29 Å3/Da / Density % sol: 46.19 % / Mosaicity: 0.665 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5M ammonium sulphate, 100mM MES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 0.9004 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2009 / Details: Vertically focussing mirror
RadiationMonochromator: Double crystal Si(111), horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9004 Å / Relative weight: 1
ReflectionRedundancy: 12.1 % / Av σ(I) over netI: 25.36 / Number: 272436 / Rmerge(I) obs: 0.092 / Χ2: 0.93 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 22544 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955099.710.0621.84810.7
3.934.9510010.0671.6189.3
3.443.9399.910.0681.13510.5
3.123.4410010.0830.91111.6
2.93.1210010.1190.77512.6
2.732.910010.1620.71313.3
2.592.7310010.2420.68413.8
2.482.5910010.3160.63914.1
2.382.4810010.4040.63813.3
2.32.3899.810.4540.6412
ReflectionResolution: 2.3→51.15 Å / Num. all: 26634 / Num. obs: 22544 / % possible obs: 99.9 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.092 / Χ2: 0.926 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.38120.45421870.64199.8
2.38-2.4813.30.40422090.6381100
2.48-2.5914.10.31621880.6391100
2.59-2.7313.80.24222010.6841100
2.73-2.913.30.16222370.7131100
2.9-3.1212.60.11922440.7751100
3.12-3.4411.60.08322430.9111100
3.44-3.9310.50.06822801.135199.9
3.93-4.959.30.06722861.6181100
4.95-5010.70.06224691.848199.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→51.15 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.2881 / WRfactor Rwork: 0.2437 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.804 / SU B: 16.404 / SU ML: 0.182 / SU R Cruickshank DPI: 0.2213 / SU Rfree: 0.2609 / Cross valid method: THROUGHOUT / ESU R: 0.357 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27772 1127 5 %RANDOM
Rwork0.22945 ---
obs0.23181 21243 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.45 Å2 / Biso mean: 43.132 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å21.23 Å20 Å2
2--2.45 Å20 Å2
3----3.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→51.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 0 161 3462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9744488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8425424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01623.121141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30815499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2491529
X-RAY DIFFRACTIONr_chiral_restr0.0740.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212519
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_it0.6061.52129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14223402
X-RAY DIFFRACTIONr_scbond_it1.45331162
X-RAY DIFFRACTIONr_scangle_it2.3524.51086
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
Rfree0.322 73 -
Rwork0.272 1546 -
all-1619 -
obs--98.72 %
Refinement TLS params.Method: refined / Origin x: 44.5552 Å / Origin y: 27.5898 Å / Origin z: 99.4467 Å
111213212223313233
T0.0878 Å2-0.0261 Å20.0127 Å2-0.0718 Å2-0.0202 Å2--0.0175 Å2
L0.2698 °20.3632 °20.2086 °2-0.7817 °20.3815 °2--0.9752 °2
S0.1084 Å °-0.0691 Å °0.0238 Å °0.0319 Å °-0.1168 Å °0.0328 Å °0.0488 Å °-0.0141 Å °0.0084 Å °

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