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- PDB-6lk3: The Functional Characterization and Crystal Structure of Type II ... -

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Basic information

Entry
Database: PDB / ID: 6lk3
TitleThe Functional Characterization and Crystal Structure of Type II Peptidyl Carrier Protein ColA1a in Collismycins Biosynthesis
ComponentsPutative free-standing acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / Biosynthesis / ColA1a / Collismycins / NRPS / Peptidyl Carrier Protein
Function / homologyPhosphopantetheine attachment site / ACP-like superfamily / Phosphopantetheine binding ACP domain / Putative free-standing acyl carrier protein
Function and homology information
Biological speciesStreptomyces sp. CS40 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMa, X.Y. / Wang, G.Y. / Liu, T. / Chi, C.B. / Zhang, Z.Y. / Yang, D.H. / Liu, W. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Chin.J.Chem. / Year: 2020
Title: The functional characterization and crystal structure of type II peptidyl carrier protein ColA1a in collismycins biosynthesis.
Authors: Ma, X.Y. / Wang, G.Y. / Liu, T. / Chi, C.B. / Zhang, Z.Y. / Yang, D.H. / Liu, W. / Ma, M.
History
DepositionDec 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative free-standing acyl carrier protein
B: Putative free-standing acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)23,7672
Polymers23,7672
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The biological assembly predicted by gel filtration is dimeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.697, 79.027, 34.088
Angle α, β, γ (deg.)90.000, 111.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative free-standing acyl carrier protein


Mass: 11883.458 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CS40 (bacteria) / Gene: clmP / Production host: Escherichia coli (E. coli) / References: UniProt: H1ZYT7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe source organism is Streptomyces roseosporus NRRL 11379. So, There is no genome sequence of ...The source organism is Streptomyces roseosporus NRRL 11379. So, There is no genome sequence of Streptomyces roseosporus NRRL 11379 in the database.

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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: 1.78 Å3/Da / Density % sol: 30.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris pH 6.25, 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.1→39.51 Å / Num. obs: 9816 / % possible obs: 98.1 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 4.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.473 / Num. unique obs: 503

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→39.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.852 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 478 5 %RANDOM
Rwork0.1493 ---
obs0.1519 9128 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.45 Å2 / Biso mean: 24.982 Å2 / Biso min: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.02 Å2
2--0.07 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 0 101 1297
Biso mean---34.87 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191205
X-RAY DIFFRACTIONr_bond_other_d0.0030.021195
X-RAY DIFFRACTIONr_angle_refined_deg1.92.0031631
X-RAY DIFFRACTIONr_angle_other_deg1.06632756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.75124.64356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98815233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6841512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02224
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.285 25 -
Rwork0.141 653 -
obs--93.26 %

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