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- PDB-7f08: Crystal Structure of K8 -

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Basic information

Entry
Database: PDB / ID: 7f08
TitleCrystal Structure of K8
Componentschalcone synthase
KeywordsHYDROLASE / chalcone synthase
Function / homologyCOENZYME A
Function and homology information
Biological speciesAbrus precatorius (Indian licorice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsHuang, S.X. / Yan, Y.J.
CitationJournal: To Be Published
Title: Crystal Structure of K8
Authors: Huang, S.X. / Yan, Y.J.
History
DepositionJun 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: chalcone synthase
D: chalcone synthase
F: chalcone synthase
H: chalcone synthase
J: chalcone synthase
L: chalcone synthase
N: chalcone synthase
P: chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,39512
Polymers344,3258
Non-polymers3,0704
Water0
1
B: chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8082
Polymers43,0411
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8082
Polymers43,0411
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: chalcone synthase


Theoretical massNumber of molelcules
Total (without water)43,0411
Polymers43,0411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: chalcone synthase


Theoretical massNumber of molelcules
Total (without water)43,0411
Polymers43,0411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
J: chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8082
Polymers43,0411
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
L: chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8082
Polymers43,0411
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
N: chalcone synthase


Theoretical massNumber of molelcules
Total (without water)43,0411
Polymers43,0411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
P: chalcone synthase


Theoretical massNumber of molelcules
Total (without water)43,0411
Polymers43,0411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.151, 117.326, 132.878
Angle α, β, γ (deg.)109.735, 90.192, 91.179
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and resid 14 through 390)
d_2ens_1(chain "D" and resid 14 through 390)
d_3ens_1chain "F"
d_4ens_1(chain "H" and resid 14 through 390)
d_5ens_1(chain "J" and resid 14 through 390)
d_6ens_1(chain "L" and resid 14 through 390)
d_7ens_1(chain "N" and resid 14 through 390)
d_8ens_1(chain "P" and resid 14 through 390)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROVALA1 - 377
d_21ens_1PROVALC1 - 377
d_31ens_1PROVALE1 - 377
d_41ens_1PROVALF3 - 379
d_51ens_1PROVALG2 - 378
d_61ens_1PROVALI1 - 377
d_71ens_1PROVALK3 - 379
d_81ens_1PROVALL1 - 377

NCS oper:
IDCodeMatrixVector
1given(0.999661065245, -0.0260109574683, -0.00108845056621), (-0.0260192533949, -0.999625583086, -0.0084671183617), (-0.000867805176327, 0.00849256923211, -0.999963560927)23.5714116628, 34.7587950137, 40.6636261504
2given(0.751673134339, 0.37033581642, 0.54574617011), (0.141446033368, 0.717697826316, -0.681837847105), (-0.644189815782, 0.589712822633, 0.487091642369)9.05075279725, -18.8025936152, -52.0286054698
3given(0.750535602344, 0.367209259352, 0.54941211259), (-0.145091721205, -0.719541236015, 0.679123554379), (0.644705127986, -0.589421555018, -0.486762291502)-17.0800140535, -18.0776879551, -32.0934734931
4given(-0.99993046212, 0.00011256541512, 0.0117922963803), (-0.0050213642417, -0.90884111763, -0.417112225673), (0.0106703714109, -0.417142433989, 0.908778483977)-13.545066559, -13.4490355496, -2.81204459495
5given(-0.99972631733, 0.0128779856435, 0.0195306918138), (0.0197626513403, 0.911655459289, 0.410479915659), (-0.0125191073549, 0.410753552673, -0.91166045813)12.646037131, -68.847370008, 43.441173926
6given(-0.736964931485, -0.568256853868, 0.36601480543), (0.168124786318, 0.37037385387, 0.913541057969), (-0.654688281541, 0.734783884147, -0.177414479711)-34.0309978875, -8.28193465018, -31.8891442771
7given(-0.740868189682, -0.568580599217, 0.357533813382), (-0.160388696483, -0.367152454135, -0.916228433014), (0.652219128482, -0.736148882779, 0.180817672878)-7.9003149499, -28.4874408837, -52.3131759791

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Components

#1: Protein
chalcone synthase /


Mass: 43040.617 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Abrus precatorius (Indian licorice) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Calcium acetate, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.16→66.49 Å / Num. obs: 80588 / % possible obs: 94.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 71.42 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.061 / Net I/σ(I): 10.9
Reflection shellResolution: 3.16→3.24 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5728 / Rpim(I) all: 0.267 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJY

4yjy


Resolution: 3.16→45.18 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.5178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 2286 5 %
Rwork0.1799 43444 -
obs0.184 45730 89.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.14 Å2
Refinement stepCycle: LAST / Resolution: 3.16→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23244 0 188 0 23432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010723896
X-RAY DIFFRACTIONf_angle_d1.393132399
X-RAY DIFFRACTIONf_chiral_restr0.073743
X-RAY DIFFRACTIONf_plane_restr0.00914128
X-RAY DIFFRACTIONf_dihedral_angle_d17.11423381
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONTorsion NCS0.58605896675
ens_1d_3FX-RAY DIFFRACTIONTorsion NCS0.633925277548
ens_1d_4HX-RAY DIFFRACTIONTorsion NCS0.615071265679
ens_1d_5JX-RAY DIFFRACTIONTorsion NCS0.619426957379
ens_1d_6LX-RAY DIFFRACTIONTorsion NCS0.58335411295
ens_1d_7NX-RAY DIFFRACTIONTorsion NCS0.688875934683
ens_1d_8PX-RAY DIFFRACTIONTorsion NCS0.636387633604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.230.3467980.26211392X-RAY DIFFRACTION46.64
3.23-3.30.38381080.26552074X-RAY DIFFRACTION68.75
3.3-3.380.37341380.2632266X-RAY DIFFRACTION76.1
3.38-3.480.32061540.2432582X-RAY DIFFRACTION84.6
3.48-3.580.31931380.21812682X-RAY DIFFRACTION90.44
3.58-3.690.32791580.20242873X-RAY DIFFRACTION94.1
3.69-3.820.26941340.20172890X-RAY DIFFRACTION96.15
3.82-3.980.27581640.1972972X-RAY DIFFRACTION97.76
3.98-4.160.26721500.17322927X-RAY DIFFRACTION97.9
4.16-4.380.21911550.17183010X-RAY DIFFRACTION98.29
4.38-4.650.24621530.15692968X-RAY DIFFRACTION98.36
4.65-5.010.23651670.14982949X-RAY DIFFRACTION98.7
5.01-5.510.2661560.16862977X-RAY DIFFRACTION98.34
5.51-6.310.2511330.17622986X-RAY DIFFRACTION98.33
6.31-7.940.26141300.16993010X-RAY DIFFRACTION98.34
7.94-45.180.19031500.1432886X-RAY DIFFRACTION95.38

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