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- PDB-3vns: Co-crystal structure of NRPS adenylation protein CytC1 with D-val... -

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Basic information

Entry
Database: PDB / ID: 3vns
TitleCo-crystal structure of NRPS adenylation protein CytC1 with D-valine and AMP from streptomyces
ComponentsNRPS adenylation protein CytC1
KeywordsLIGASE / Adenylation / ATP-binding / Non-ribosomal peptide synthese / NRPS / Streptomyces
Function / homologyANL, C-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE MONOPHOSPHATE / D-VALINE
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsOkumura, H. / Ueki, M. / Shiro, Y. / Osada, H.
CitationJournal: to be published
Title: Substrate recognition mechanism of NRPS adenylation protein from Streptomyces
Authors: Ueki, M. / Okumura, H. / Osada, H.
History
DepositionJan 17, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NRPS adenylation protein CytC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4573
Polymers58,9931
Non-polymers4642
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.544, 156.544, 156.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-749-

HOH

21A-767-

HOH

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Components

#1: Protein NRPS adenylation protein CytC1


Mass: 58992.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: RK95-74 / Production host: Escherichia coli (E. coli)
#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-DVA / D-VALINE


Type: D-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1M ammonium sulfate, 24-32% PEG5000 monomethyl ether, 1mM ATP, 100mM Hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2006 / Details: mirrors
Diffraction measurementDetails: 1.00 degrees, 12.0 sec, detector distance 160.00 mm
Method: \w scans
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.062 / Number: 971102
ReflectionResolution: 2→50 Å / Num. obs: 43061 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 22.6 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 70.394
Reflection shellResolution: 2→2.03 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 8.185 / Rsym value: 0.461 / % possible all: 100
Cell measurementReflection used: 971102

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMU

1amu


Resolution: 2.001→39.136 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.25 / σ(F): 0 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 2175 5.06 %RANDOM
Rwork0.1914 ---
obs0.1926 42998 99.94 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.655 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 86.47 Å2 / Biso mean: 30.0518 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.001→39.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 31 278 4114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053919
X-RAY DIFFRACTIONf_angle_d1.0125342
X-RAY DIFFRACTIONf_chiral_restr0.068607
X-RAY DIFFRACTIONf_plane_restr0.004695
X-RAY DIFFRACTIONf_dihedral_angle_d12.2821419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0011-2.04460.26891370.223425412678100
2.0446-2.09210.25481430.202425282671100
2.0921-2.14440.2461500.199825482698100
2.1444-2.20240.22741170.192825222639100
2.2024-2.26720.25051330.192425272660100
2.2672-2.34040.25481090.198925712680100
2.3404-2.4240.22871410.197925182659100
2.424-2.52110.26221350.200625502685100
2.5211-2.63580.25421410.213325252666100
2.6358-2.77470.2521350.208225472682100
2.7747-2.94850.23061270.205125772704100
2.9485-3.17610.22421440.20525272671100
3.1761-3.49550.2141460.206325522698100
3.4955-4.00090.19081440.174325462690100
4.0009-5.0390.14461290.156626092738100
5.039-39.14350.21081440.18792635277999

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