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- PDB-7w5u: Acetyl-CoA Carboxylase-AccB -

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Basic information

Entry
Database: PDB / ID: 7w5u
TitleAcetyl-CoA Carboxylase-AccB
ComponentsAcetyl-CoA carboxylase complex, beta-chain
KeywordsTRANSFERASE / OvmG / Streptomyces / Acetyl-CoA Carboxylase / Carboxyl Transferase
Function / homology
Function and homology information


: / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Acetyl-CoA carboxylase complex, beta-chain
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsAli, I. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770068, 32070040, 31800045 China
CitationJournal: Comput Biol Med / Year: 2022
Title: Crystal structure of Acetyl-CoA carboxylase (AccB) from Streptomyces antibioticus and insights into the substrate-binding through in silico mutagenesis and biophysical investigations.
Authors: Ali, I. / Khan, A. / Fa, Z. / Khan, T. / Wei, D.Q. / Zheng, J.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-CoA carboxylase complex, beta-chain
B: Acetyl-CoA carboxylase complex, beta-chain
C: Acetyl-CoA carboxylase complex, beta-chain
D: Acetyl-CoA carboxylase complex, beta-chain
E: Acetyl-CoA carboxylase complex, beta-chain
F: Acetyl-CoA carboxylase complex, beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,86016
Polymers334,9156
Non-polymers94510
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43350 Å2
ΔGint-341 kcal/mol
Surface area98720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.001, 202.390, 204.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acetyl-CoA carboxylase complex, beta-chain


Mass: 55819.168 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Streptomyces antibioticus (bacteria) / References: UniProt: Q6ZZV4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: SaltRx TM, HR2-909-20,0.8 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS propane. pH 7.0
PH range: 7.0 -7.5 / Temp details: 3 weeks in incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.34→39.74 Å / Num. obs: 204886 / % possible obs: 98.9 % / Redundancy: 5.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.044 / Rrim(I) all: 0.114 / Net I/σ(I): 7.4
Reflection shellResolution: 2.34→2.34 Å / Redundancy: 5.9 % / Num. unique obs: 192724 / CC1/2: 0.986 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-20002.3.12data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XNV

1xnv


Resolution: 2.34→39.74 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.123 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23929 10132 5 %RANDOM
Rwork0.2173 ---
obs0.2184 192724 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.85 Å2 / Biso mean: 41.123 Å2 / Biso min: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.34→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23450 0 54 99 23603
Biso mean--54.93 31.54 -
Num. residues----3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01323960
X-RAY DIFFRACTIONr_bond_other_d0.0010.01722422
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.64332492
X-RAY DIFFRACTIONr_angle_other_deg1.2841.57851734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86253072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31320.9781350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.346153876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.64215234
X-RAY DIFFRACTIONr_chiral_restr0.0720.23096
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0227534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025160
LS refinement shellResolution: 2.34→2.399 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.381 717 -
Rwork0.342 13157 -
obs--92.7 %

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