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- PDB-5vcb: Crystal structure of holo-(acyl-carrier-protein) synthase:holo(ac... -

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Basic information

Entry
Database: PDB / ID: 5vcb
TitleCrystal structure of holo-(acyl-carrier-protein) synthase:holo(acyl-carrier-protein) complex from Escherichia Coli.
Components
  • Acyl carrier protein
  • Holo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / Hexamer Product Complex
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / fatty acid biosynthetic process / transferase activity / response to xenobiotic stimulus ...holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / fatty acid biosynthetic process / transferase activity / response to xenobiotic stimulus / lipid binding / magnesium ion binding / cytosol / cytoplasm
Similarity search - Function
Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily ...Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / Acyl carrier protein / Acyl carrier protein / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsMarcella, A.M. / Barb, A.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)EEC-0813570 United States
Argonne National Laboratory's (Beam time)GUP-48455 United States
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structure, High Affinity, and Negative Cooperativity of the Escherichia coli Holo-(Acyl Carrier Protein):Holo-(Acyl Carrier Protein) Synthase Complex.
Authors: Marcella, A.M. / Culbertson, S.J. / Shogren-Knaak, M.A. / Barb, A.W.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
b: Holo-[acyl-carrier-protein] synthase
a: Holo-[acyl-carrier-protein] synthase
c: Holo-[acyl-carrier-protein] synthase
f: Acyl carrier protein
e: Acyl carrier protein
d: Acyl carrier protein
G: Holo-[acyl-carrier-protein] synthase
I: Holo-[acyl-carrier-protein] synthase
H: Holo-[acyl-carrier-protein] synthase
K: Acyl carrier protein
J: Acyl carrier protein
L: Acyl carrier protein
O: Holo-[acyl-carrier-protein] synthase
N: Holo-[acyl-carrier-protein] synthase
M: Holo-[acyl-carrier-protein] synthase
F: Acyl carrier protein
E: Acyl carrier protein
D: Acyl carrier protein
B: Holo-[acyl-carrier-protein] synthase
A: Holo-[acyl-carrier-protein] synthase
C: Holo-[acyl-carrier-protein] synthase
P: Acyl carrier protein
R: Acyl carrier protein
Q: Acyl carrier protein
T: Holo-[acyl-carrier-protein] synthase
S: Holo-[acyl-carrier-protein] synthase
U: Holo-[acyl-carrier-protein] synthase
X: Acyl carrier protein
W: Acyl carrier protein
V: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,66944
Polymers341,65230
Non-polymers5,01714
Water00
1
b: Holo-[acyl-carrier-protein] synthase
a: Holo-[acyl-carrier-protein] synthase
c: Holo-[acyl-carrier-protein] synthase
f: Acyl carrier protein
e: Acyl carrier protein
d: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4059
Polymers68,3306
Non-polymers1,0753
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Holo-[acyl-carrier-protein] synthase
I: Holo-[acyl-carrier-protein] synthase
H: Holo-[acyl-carrier-protein] synthase
K: Acyl carrier protein
J: Acyl carrier protein
L: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0478
Polymers68,3306
Non-polymers7172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
O: Holo-[acyl-carrier-protein] synthase
N: Holo-[acyl-carrier-protein] synthase
M: Holo-[acyl-carrier-protein] synthase
P: Acyl carrier protein
R: Acyl carrier protein
Q: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4059
Polymers68,3306
Non-polymers1,0753
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Acyl carrier protein
E: Acyl carrier protein
D: Acyl carrier protein
B: Holo-[acyl-carrier-protein] synthase
A: Holo-[acyl-carrier-protein] synthase
C: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4059
Polymers68,3306
Non-polymers1,0753
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
T: Holo-[acyl-carrier-protein] synthase
S: Holo-[acyl-carrier-protein] synthase
U: Holo-[acyl-carrier-protein] synthase
X: Acyl carrier protein
W: Acyl carrier protein
V: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4059
Polymers68,3306
Non-polymers1,0753
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)251.424, 251.424, 58.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Holo-[acyl-carrier-protein] synthase / Holo-ACP synthase / 4'-phosphopantetheinyl transferase AcpS


Mass: 14074.297 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acpS, dpj, b2563, JW2547 / Production host: Escherichia coli (E. coli)
References: UniProt: P24224, holo-[acyl-carrier-protein] synthase
#2: Protein
Acyl carrier protein / ACP


Mass: 8702.512 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: acpP, ECS88_1108 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MJ81, UniProt: P0A6A8*PLUS
#3: Chemical
ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C11H23N2O7PS

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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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris propane, pH 7.0 18-22% PEG 6k or 18-22% PEG 10k

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→49.308 Å / Num. obs: 28625 / % possible obs: 95.6 % / Redundancy: 5.8 % / CC1/2: 0.989 / Rmerge(I) obs: 0.247 / Net I/σ(I): 5
Reflection shellHighest resolution: 4.1 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3890 / CC1/2: 0.251 / % possible all: 80.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VBX

5vbx


Resolution: 4.1→49.308 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2968 1396 4.88 %
Rwork0.2782 --
obs0.2791 28625 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→49.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23247 0 111 0 23358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423758
X-RAY DIFFRACTIONf_angle_d0.99632098
X-RAY DIFFRACTIONf_dihedral_angle_d18.4128711
X-RAY DIFFRACTIONf_chiral_restr0.0643685
X-RAY DIFFRACTIONf_plane_restr0.0054181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1003-4.24680.3765970.38342376X-RAY DIFFRACTION85
4.2468-4.41670.38051510.38882511X-RAY DIFFRACTION91
4.4167-4.61760.37441420.3842673X-RAY DIFFRACTION96
4.6176-4.86080.39021370.35692760X-RAY DIFFRACTION98
4.8608-5.16510.33531410.3342767X-RAY DIFFRACTION99
5.1651-5.56340.37891370.3392781X-RAY DIFFRACTION99
5.5634-6.12230.37671520.33872769X-RAY DIFFRACTION99
6.1223-7.00610.31541660.2932811X-RAY DIFFRACTION99
7.0061-8.81870.27621490.2412829X-RAY DIFFRACTION99
8.8187-49.31180.20011240.19652952X-RAY DIFFRACTION98

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