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- PDB-3vnq: Co-crystal structure of NRPS adenylation protein CytC1 with ATP f... -

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Basic information

Entry
Database: PDB / ID: 3vnq
TitleCo-crystal structure of NRPS adenylation protein CytC1 with ATP from streptomyces
ComponentsNRPS adenylation protein CytC1
KeywordsLIGASE / Adenylation / ATP-binding / Non-ribosomal peptide synthese / NRPS / Streptomyces
Function / homologyANL, N-terminal domain / ANL, C-terminal domain / GMP Synthetase; Chain A, domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 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

Downloads & links

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Assembly

Deposited unit
A: NRPS adenylation protein CytC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5002
Polymers58,9931
Non-polymers5071
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.146, 156.146, 156.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

21A-924-

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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
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: Dec 14, 2006 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 37003 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 27.52 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 53.384
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 7.878 / Rsym value: 0.405 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMU

1amu


Resolution: 2.1→34.915 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8579 / SU ML: 0.26 / σ(F): 0 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1853 5.01 %RANDOM
Rwork0.184 ---
obs0.1858 36956 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.447 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 89.75 Å2 / Biso mean: 31.1802 Å2 / Biso min: 11.18 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 31 281 4117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093920
X-RAY DIFFRACTIONf_angle_d1.35348
X-RAY DIFFRACTIONf_chiral_restr0.083606
X-RAY DIFFRACTIONf_plane_restr0.006694
X-RAY DIFFRACTIONf_dihedral_angle_d13.6991420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.15690.25581530.184326842837100
2.1569-2.22040.22921250.190727192844100
2.2204-2.2920.27151240.211726782802100
2.292-2.37390.24251270.191426772804100
2.3739-2.46890.2261500.181526822832100
2.4689-2.58130.28651530.198526522805100
2.5813-2.71730.2721520.203226702822100
2.7173-2.88750.26511320.196227172849100
2.8875-3.11030.22461410.204726922833100
3.1103-3.42310.24811530.199926992852100
3.4231-3.91780.19461570.177927032860100
3.9178-4.93380.1651310.148927422873100
4.9338-34.92010.19371550.17772788294399

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