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- PDB-4u5q: High resolution crystal structure of reductase (R) domain of nonr... -

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Basic information

Entry
Database: PDB / ID: 4u5q
TitleHigh resolution crystal structure of reductase (R) domain of nonribosomal peptide synthetase from Mycobacterium tuberculosis
ComponentsPeptide synthetase
KeywordsLIGASE / nonribosomal peptide synthetase / oxidoreductase / Short-chain dehydrogenase/reductase
Function / homology
Function and homology information


Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / ligase activity / phosphopantetheine binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / transferase activity / ATP binding ...Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / ligase activity / phosphopantetheine binding / 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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 1.811 Å
AuthorsPatel, K.D. / Haque, A.S. / Priyadarshan, K. / Sankaranarayanan, R.
Citation
Journal: To Be Published
Title: High resolution structure of R-domain of nonribosomal peptide synthetase from Mycobacterium tuberculosis
Authors: Patel, K.D. / Haque, A.S. / Sankaranarayanan, R.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / 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
DepositionJul 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide synthetase
B: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9733
Polymers104,5142
Non-polymers4591
Water10,989610
1
A: Peptide synthetase


Theoretical massNumber of molelcules
Total (without water)52,2571
Polymers52,2571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7162
Polymers52,2571
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.532, 88.593, 126.077
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 Peptide synthetase / Probable peptide synthetase Nrp (Peptide synthase)


Mass: 52257.004 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2056-2512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: nrp, Rv0101, LH57_00575 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q10896
#2: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NaCl, 0.1 M HEPES pH 7.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 20, 2010
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.81→42.99 Å / Num. obs: 80272 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rsym value: 0.085 / Net I/σ(I): 19.36
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.58 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQV

4dqv


Resolution: 1.811→42.985 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 4024 5.03 %
Rwork0.2023 --
obs0.2045 80071 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.811→42.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6598 0 31 610 7239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066763
X-RAY DIFFRACTIONf_angle_d0.8219197
X-RAY DIFFRACTIONf_dihedral_angle_d11.3014077
X-RAY DIFFRACTIONf_chiral_restr0.0511056
X-RAY DIFFRACTIONf_plane_restr0.0051200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8108-1.83210.2941300.24482324X-RAY DIFFRACTION90
1.8321-1.85440.33181350.24632607X-RAY DIFFRACTION100
1.8544-1.87790.28571370.25212626X-RAY DIFFRACTION100
1.8779-1.90260.30731290.23972592X-RAY DIFFRACTION100
1.9026-1.92870.32631340.26012604X-RAY DIFFRACTION100
1.9287-1.95620.29161270.23732611X-RAY DIFFRACTION100
1.9562-1.98540.26981340.2162587X-RAY DIFFRACTION100
1.9854-2.01650.29491320.21182647X-RAY DIFFRACTION100
2.0165-2.04950.23591430.20162579X-RAY DIFFRACTION100
2.0495-2.08490.26011220.19492655X-RAY DIFFRACTION100
2.0849-2.12280.22631420.19672619X-RAY DIFFRACTION100
2.1228-2.16360.24571310.20032593X-RAY DIFFRACTION100
2.1636-2.20780.23351570.1972594X-RAY DIFFRACTION100
2.2078-2.25580.24981370.21952627X-RAY DIFFRACTION100
2.2558-2.30820.25871350.20772601X-RAY DIFFRACTION99
2.3082-2.3660.2441570.19532620X-RAY DIFFRACTION100
2.366-2.42990.24061260.20072621X-RAY DIFFRACTION100
2.4299-2.50140.25581510.20742598X-RAY DIFFRACTION100
2.5014-2.58210.26481360.21382653X-RAY DIFFRACTION100
2.5821-2.67440.25381350.22572617X-RAY DIFFRACTION100
2.6744-2.78150.2991330.22322645X-RAY DIFFRACTION100
2.7815-2.9080.2841340.21852645X-RAY DIFFRACTION99
2.908-3.06130.25821300.22012641X-RAY DIFFRACTION99
3.0613-3.25310.26741260.21012651X-RAY DIFFRACTION100
3.2531-3.50410.2721470.18922668X-RAY DIFFRACTION100
3.5041-3.85660.24071400.18122667X-RAY DIFFRACTION99
3.8566-4.41410.18431520.16772667X-RAY DIFFRACTION99
4.4141-5.55950.20411630.18632695X-RAY DIFFRACTION99
5.5595-42.99750.22081690.19382793X-RAY DIFFRACTION99

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