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- PDB-4neo: Structure of BlmI, a type-II acyl-carrier-protein from Streptomyc... -

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Basic information

Entry
Database: PDB / ID: 4neo
TitleStructure of BlmI, a type-II acyl-carrier-protein from Streptomyces verticillus involved in bleomycin biosynthesis
ComponentsPeptide synthetase NRPS type II-PCP
KeywordsLIGASE / Structural Genomics / PSI-Biology / Enzyme Discovery for Natural Product Biosynthesis / NatPro / peptide synthetase / BIOSYNTHETIC PROTEIN / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


non-ribosomal peptide synthetase activity / phosphopantetheine binding
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain ...ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peptide synthetase NRPS type II-PCP
Similarity search - Component
Biological speciesStreptomyces verticillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCuff, M.E. / Bigelow, L. / Bearden, J. / Babnigg, G. / Bruno, C.J.P. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. ...Cuff, M.E. / Bigelow, L. / Bearden, J. / Babnigg, G. / Bruno, C.J.P. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2014
Title: The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins.
Authors: Lohman, J.R. / Ma, M. / Cuff, M.E. / Bigelow, L. / Bearden, J. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionOct 29, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 29, 2014ID: 4I4D
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Structure summary
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Sep 3, 2014Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Mar 22, 2023Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Peptide synthetase NRPS type II-PCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5503
Polymers10,3671
Non-polymers1822
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.441, 73.441, 43.331
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Peptide synthetase NRPS type II-PCP


Mass: 10367.317 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces verticillus (bacteria) / Gene: blmI / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: Q9XC48
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: protein was reductively methylated, & crystallized in 0.1M CHES:NaOH pH 9.5, 30% PEG 400 , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 27, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionRedundancy: 7.1 % / Number: 56933 / Rmerge(I) obs: 0.07 / Χ2: 1.77 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 8055 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.75096.410.0716.3475.8
4.525.799.810.0624.5646.8
3.954.5299.510.0553.0336.8
3.593.9599.510.0592.8657
3.333.5910010.0632.6547.2
3.143.3310010.0742.5057.2
2.983.1410010.082.0557.2
2.852.9810010.0931.7677.3
2.742.8510010.1051.4167.3
2.652.7410010.1081.1957.3
2.562.6510010.1151.0517.3
2.492.5610010.1271.0227.3
2.422.4910010.1520.8927.3
2.372.4210010.1580.7597.3
2.312.3710010.2030.7147.3
2.262.3110010.2640.7087.3
2.222.2610010.3270.6317.3
2.182.2210010.2980.597.3
2.142.1810010.3410.6816.7
2.12.1410010.4290.5536.3
ReflectionResolution: 2.1→50 Å / Num. all: 8055 / Num. obs: 8055 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.429 / Num. unique all: 397 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.1 Å / D res low: 50 Å / FOM : 0.273 / FOM acentric: 0.31 / FOM centric: 0 / Reflection: 8041 / Reflection acentric: 7089 / Reflection centric: 952
Phasing MAD setR cullis acentric: 1.54 / R cullis centric: 1 / Highest resolution: 2.1 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 7089 / Reflection centric: 952
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.98-501.560.40.22215
7.46-12.981.050.30.210749
5.23-7.461.260.20.128779
4.03-5.231.160.20.1530101
3.28-4.031.140.10.1858137
2.76-3.281.94001270157
2.39-2.765.08001756200
2.1-2.397.77002259214
Phasing MAD set siteAtom type symbol: Se / B iso: 63.7551 / Fract x: -0.34 / Fract y: -0.506 / Fract z: -0.007 / Occupancy: 5.185 / Occupancy iso: 0
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.98-500.2260.3810372215
7.46-12.980.3130.457015610749
5.23-7.460.4080.52036628779
4.03-5.230.4030.4790631530101
3.28-4.030.4120.4780995858137
2.76-3.280.3980.447014271270157
2.39-2.760.2550.284019561756200
2.1-2.390.1060.116024732259214
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 8041
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.42-10064.40.826501
4.27-5.4263.40.914504
3.72-4.2759.30.925505
3.37-3.7258.80.914503
3.12-3.3757.70.92514
2.93-3.1255.20.906503
2.79-2.9362.50.879505
2.66-2.7964.20.88501
2.56-2.6660.60.886505
2.47-2.5665.60.899502
2.39-2.4764.10.89502
2.32-2.3968.20.885502
2.26-2.3273.50.862506
2.2-2.2675.20.874501
2.1-2.281.20.85987

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2158 / WRfactor Rwork: 0.1893 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8949 / SU B: 7.884 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1503 / SU Rfree: 0.1322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.132
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 371 4.6 %RANDOM
Rwork0.1799 ---
all0.1808 8041 --
obs0.1808 8041 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.17 Å2 / Biso mean: 63.2554 Å2 / Biso min: 37.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.29 Å2-0 Å2
2--0.59 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms637 0 12 31 680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019707
X-RAY DIFFRACTIONr_bond_other_d0.0010.02693
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.961960
X-RAY DIFFRACTIONr_angle_other_deg0.86231581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.789592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59121.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31415111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0271511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02813
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02168
X-RAY DIFFRACTIONr_mcbond_it3.2693.925353
X-RAY DIFFRACTIONr_mcbond_other3.2633.914352
X-RAY DIFFRACTIONr_mcangle_it4.5895.826447
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 24 -
Rwork0.206 553 -
all-577 -
obs--97.14 %
Refinement TLS params.Method: refined / Origin x: 32.0853 Å / Origin y: 29.9073 Å / Origin z: -1.6628 Å
111213212223313233
T0.033 Å2-0.0333 Å20.0105 Å2-0.1167 Å20.0138 Å2--0.0438 Å2
L5.8503 °2-3.6795 °20.7254 °2-6.7594 °20.7056 °2--5.994 °2
S0.2636 Å °0.1387 Å °0.3334 Å °-0.0843 Å °-0.3044 Å °0.0604 Å °0.094 Å °0.2874 Å °0.0408 Å °

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