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- PDB-4dg8: Structure of PA1221, an NRPS protein containing adenylation and P... -

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Basic information

Entry
Database: PDB / ID: 4dg8
TitleStructure of PA1221, an NRPS protein containing adenylation and PCP domains
ComponentsPA1221
KeywordsLIGASE / ANL Superfamily / Adenylation domain / peptidyl carrier protein / Non-ribosomal peptide synthetase / NRPS / valine adenylation
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / cytoplasm
Similarity search - Function
ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site ...ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / (R,R)-2,3-BUTANEDIOL / Carrier domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMitchell, C.A. / Shi, C. / Aldrich, C.C. / Gulick, A.M.
CitationJournal: Biochemistry / Year: 2012
Title: Structure of PA1221, a Nonribosomal Peptide Synthetase Containing Adenylation and Peptidyl Carrier Protein Domains.
Authors: Mitchell, C.A. / Shi, C. / Aldrich, C.C. / Gulick, A.M.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: PA1221
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3854
Polymers67,8571
Non-polymers5273
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.565, 92.565, 164.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PA1221


Mass: 67857.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA1221 / Plasmid: pET15bTEVp21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9I4B7, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5-4 % PEG8000, 50 mM MES, 100 mM Glycine, 1 mM ATP, 1 mM Valine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2010 / Details: SSRL.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 39581 / Num. obs: 36771 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.7
Reflection shellResolution: 2.15→2.25 Å / Rmerge(I) obs: 0.481 / % possible all: 97.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AMU

1amu


Resolution: 2.15→29.38 Å / SU ML: 0.65 / σ(F): 1.33 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1862 5.06 %RANDOM
Rwork0.1861 ---
obs0.1885 36768 92.83 %-
all-39578 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.517 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4555 Å20 Å2-0 Å2
2--2.4555 Å20 Å2
3----4.9111 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 35 245 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093890
X-RAY DIFFRACTIONf_angle_d1.275302
X-RAY DIFFRACTIONf_dihedral_angle_d12.6691413
X-RAY DIFFRACTIONf_chiral_restr0.095602
X-RAY DIFFRACTIONf_plane_restr0.007698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20810.28761420.23182771X-RAY DIFFRACTION98
2.2081-2.27310.50661420.36332169X-RAY DIFFRACTION77
2.2731-2.34640.29531220.25352776X-RAY DIFFRACTION97
2.3464-2.43020.27661470.19732794X-RAY DIFFRACTION98
2.4302-2.52750.22791430.1882773X-RAY DIFFRACTION97
2.5275-2.64240.25351440.20662777X-RAY DIFFRACTION97
2.6424-2.78170.27691610.22512586X-RAY DIFFRACTION91
2.7817-2.95580.25781380.19262779X-RAY DIFFRACTION97
2.9558-3.18380.21441620.17342785X-RAY DIFFRACTION96
3.1838-3.50370.26351600.18162526X-RAY DIFFRACTION88
3.5037-4.00960.23321180.17682459X-RAY DIFFRACTION84
4.0096-5.04750.16531350.14082817X-RAY DIFFRACTION94
5.0475-29.38260.1591480.1652894X-RAY DIFFRACTION92
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)
14.28953.7656-0.87166.0819-1.61381.0640.0834-0.47260.1220.4589-0.20860.0343-0.05340.31620.090.08290.06690.0120.28170.01010.1049.814113.894136.1021
22.87322.0256-1.80632.1928-1.63612.8441-0.2465-0.0767-0.57720.08150.0495-0.27230.12290.04950.21870.17440.03620.04890.1622-0.00130.220813.5214.307424.6547
31.29030.6047-0.2752.6198-0.40074.6613-0.13160.2282-0.204-0.13080.0895-0.02810.3732-0.18590.00210.0897-0.02180.03680.1559-0.01490.147211.11336.359415.49
41.882-0.0972-0.11241.1090.00770.9995-0.0207-0.01890.272-0.05610.04530.0183-0.0806-0.0365-0.02160.11170.0031-0.00730.1435-0.00290.1014-1.01125.406926.9092
52.6128-0.0682-1.12591.62090.90872.10710.00670.41330.4391-0.07250.02380.0217-0.1961-0.2936-0.00160.2168-0.0132-0.02050.17440.09820.2890.078435.291616.5311
60.9947-1.07431.39694.4697-1.00432.04280.33190.7165-0.0659-0.1057-0.13540.43830.2133-0.544-0.16030.2927-0.00970.03750.73260.04870.2573-8.53622.7945-1.5363
75.6929-3.00910.19935.91850.26864.24070.10760.64860.1248-0.2733-0.35530.99-1.0827-0.84530.28560.46290.1563-0.06770.79980.00980.5368-17.148329.0381-2.5058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 15:48)
2X-RAY DIFFRACTION2chain 'A' and (resseq 49:85)
3X-RAY DIFFRACTION3chain 'A' and (resseq 86:156)
4X-RAY DIFFRACTION4chain 'A' and (resseq 157:388)
5X-RAY DIFFRACTION5chain 'A' and (resseq 389:437)
6X-RAY DIFFRACTION6chain 'A' and (resseq 438:481)
7X-RAY DIFFRACTION7chain 'A' and (resseq 482:511)

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