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- PDB-4gr4: Crystal structure of SlgN1deltaAsub -

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Basic information

Entry
Database: PDB / ID: 4gr4
TitleCrystal structure of SlgN1deltaAsub
ComponentsNon-ribosomal peptide synthetase
KeywordsLIGASE / MbtH-like domain / adenylation domain / Rossmann fold / ATP Binding
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / methyltransferase activity / cytosol
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Uroporphyrin-III C-methyltransferase signature 2. / Uroporphiryn-III C-methyltransferase, conserved site / ANL, N-terminal domain / Amino acid adenylation domain ...Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Uroporphyrin-III C-methyltransferase signature 2. / Uroporphiryn-III C-methyltransferase, conserved site / ANL, N-terminal 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 / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesStreptomyces lydicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsHerbst, D.A. / Zocher, G. / Stehle, T.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis of the Interaction of MbtH-like Proteins, Putative Regulators of Nonribosomal Peptide Biosynthesis, with Adenylating Enzymes.
Authors: Herbst, D.A. / Boll, B. / Zocher, G. / Stehle, T. / Heide, L.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Non-ribosomal peptide synthetase
B: Non-ribosomal peptide synthetase
C: Non-ribosomal peptide synthetase
D: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,9215
Polymers196,8854
Non-polymers351
Water7,963442
1
A: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)49,2211
Polymers49,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2572
Polymers49,2211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)49,2211
Polymers49,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)49,2211
Polymers49,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.110, 148.610, 109.580
Angle α, β, γ (deg.)90.00, 113.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Non-ribosomal peptide synthetase


Mass: 49221.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lydicus (bacteria) / Gene: slgN1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) ybdz- / References: UniProt: D1GLU5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 100 mM Tris-HCl, 0.2 M Li2SO4, 1.3 M K/Na tartrate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 9, 2011
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.44→47.65 Å / Num. all: 96463 / Num. obs: 95771 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.35 Å2
Reflection shellResolution: 2.44→2.5 Å / Mean I/σ(I) obs: 1.84 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→35.72 Å / Cor.coef. Fo:Fc: 0.9336 / Cor.coef. Fo:Fc free: 0.9111 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 4790 5 %RANDOM
Rwork0.1804 ---
obs0.1821 95737 99.63 %-
all-96463 --
Displacement parametersBiso mean: 43.52 Å2
Baniso -1Baniso -2Baniso -3
1--5.3825 Å20 Å23.8221 Å2
2--3.5906 Å20 Å2
3---1.7919 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: LAST / Resolution: 2.44→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13340 0 1 442 13783
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113663HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1718629HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4387SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes261HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2107HARMONIC5
X-RAY DIFFRACTIONt_it13663HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion19.18
X-RAY DIFFRACTIONt_chiral_improper_torsion1696SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15256SEMIHARMONIC4
LS refinement shellResolution: 2.44→2.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2672 325 4.68 %
Rwork0.2208 6614 -
all0.223 6939 -
obs--99.63 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.81920.00490.28811.19710.3611.3177-0.0001-0.1321-0.02310.1312-0.0469-0.01080.1111-0.12820.047-0.1185-0.0381-0.0183-0.06190.0078-0.0885-15.306423.1979-26.3067
21.0051-0.08550.0861.28660.17751.30420.0246-0.11970.02580.2422-0.09160.0589-0.0122-0.06310.067-0.0416-0.0320.0309-0.1280.0107-0.12132.2468-19.7637-16.0791
30.97480.31540.20021.4520.27691.49420.01490.1944-0.0167-0.17330.04910.05050.13670.0236-0.0639-0.07410.0179-0.0377-0.10930.016-0.1281-40.743512.6377-75.2446
41.1926-0.0289-0.53631.52450.07371.6786-0.00040.1626-0.0258-0.2210.00790.093-0.0637-0.1287-0.0075-0.15690.0305-0.023-0.0909-0.0063-0.1141-57.6053-31.2568-63.3344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 466
2X-RAY DIFFRACTION2B0 - 466
3X-RAY DIFFRACTION3C3 - 465
4X-RAY DIFFRACTION4D2 - 466

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