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- PDB-8gx4: Crystal structure of Diels-Alderase ApiI in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 8gx4
TitleCrystal structure of Diels-Alderase ApiI in complex with SAM
ComponentsApiI
KeywordsBIOSYNTHETIC PROTEIN
Function / homologyTRIETHYLENE GLYCOL / S-ADENOSYLMETHIONINE
Function and homology information
Biological speciesApiospora montagnei NRRL 25634 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97007775894 Å
AuthorsZhou, J.H. / Lu, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91856202 China
CitationJournal: To Be Published
Title: Crystal structure of Diels-Alderase ApiI in complex with SAM
Authors: Zhou, J.H. / Lu, J.Y.
History
DepositionSep 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ApiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5698
Polymers43,6801
Non-polymers8897
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.340, 98.340, 80.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ApiI


Mass: 43680.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apiospora montagnei NRRL 25634 (fungus)
Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 168 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES/NaOH PH=7.0, 0.2 M NaCl, 20%(w/v)PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.97→23.51 Å / Num. obs: 32051 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 36.067981888 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.025 / Rrim(I) all: 0.08 / Net I/σ(I): 25.2
Reflection shellResolution: 1.97→2.02 Å / Rmerge(I) obs: 1.267 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 318124 / CC1/2: 0.882 / Rpim(I) all: 0.462 / Rrim(I) all: 1.35

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WUP

7wup


Resolution: 1.97007775894→21.291234552 Å / SU ML: 0.220133981946 / Cross valid method: FREE R-VALUE / σ(F): 1.34219864499 / Phase error: 25.252094625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244781446514 1511 4.72364636739 %
Rwork0.206412791754 30477 -
obs0.208163646967 31988 99.641778027 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.8281266322 Å2
Refinement stepCycle: LAST / Resolution: 1.97007775894→21.291234552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 59 161 3172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007625086830673057
X-RAY DIFFRACTIONf_angle_d0.9061327300084133
X-RAY DIFFRACTIONf_chiral_restr0.0535590922993480
X-RAY DIFFRACTIONf_plane_restr0.00640556703369529
X-RAY DIFFRACTIONf_dihedral_angle_d4.249555327661862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9701-2.03360.3039470213591700.2507407781832698X-RAY DIFFRACTION99.8259658893
2.0336-2.10620.317877026651370.300204274942730X-RAY DIFFRACTION99.7911590672
2.1062-2.19050.2725488221621320.2418125255512792X-RAY DIFFRACTION99.795221843
2.1905-2.29010.4433525054461530.2932854616392624X-RAY DIFFRACTION96.8946266574
2.2901-2.41070.2659538895391490.2232561020582745X-RAY DIFFRACTION99.9654576857
2.4107-2.56150.228689928314930.2126880668892781X-RAY DIFFRACTION99.9304589708
2.5615-2.75880.3069738568481350.2239339235142792X-RAY DIFFRACTION99.9658469945
2.7588-3.03580.2564002455451540.2177670097142750X-RAY DIFFRACTION100
3.0358-3.47340.2602190596261370.2140050328242798X-RAY DIFFRACTION100
3.4734-4.36990.1987098969941270.1868234284012831X-RAY DIFFRACTION99.9662047989

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