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- PDB-6j03: Crystal structure of a cyclase mutant in apo form -

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Basic information

Entry
Database: PDB / ID: 6j03
TitleCrystal structure of a cyclase mutant in apo form
Components12-epi-hapalindole U synthase
KeywordsTRANSFERASE / prenyltransferase / mutation
Function / homology: / HpiC1 cyclase / metal ion binding / Chem-0HZ / 12-epi-hapalindole U synthase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsTang, X.K. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Rsc Adv / Year: 2019
Title: Structural insights into the calcium dependence of Stig cyclases.
Authors: Tang, X.K. / Xue, J. / Yang, Y.Y. / Ko, T.P. / Chen, C.Y. / Dai, L.H. / Guo, R.T. / Zhang, Y.H. / Chen, C.C.
History
DepositionDec 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 12-epi-hapalindole U synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0383
Polymers21,7441
Non-polymers2942
Water5,963331
1
A: 12-epi-hapalindole U synthase
hetero molecules

A: 12-epi-hapalindole U synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0776
Polymers43,4882
Non-polymers5894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_767-x+2,-x+y+1,-z+7/31
Buried area1700 Å2
ΔGint-6 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.779, 54.779, 152.416
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 12-epi-hapalindole U synthase / AmbU4


Mass: 21744.029 Da / Num. of mol.: 1 / Fragment: UNP residues 35-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V5TER4
#2: Chemical ChemComp-0HZ / amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium / CI-4 / [cyclo-(l-Arg-d-Pro)]


Type: peptide-like / Mass: 254.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3.04 Å3/Da / Density % sol: 59.49 % / Mosaicity: 0.208 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350, Tryptone, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→25 Å / Num. obs: 44964 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.022 / Rrim(I) all: 0.043 / Χ2: 0.795 / Net I/σ(I): 13.4 / Num. measured all: 168760
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.48-1.5330.243140.9380.1330.2420.46398.2
1.53-1.593.90.16443920.9760.0940.190.46899.3
1.59-1.673.90.13144560.9840.0760.1520.51499.5
1.67-1.753.90.09444600.9910.0540.1090.57499.6
1.75-1.863.90.06844380.9950.0390.0780.65999.8
1.86-2.013.90.04844740.9970.0280.0550.80499.8
2.01-2.213.90.03845170.9980.0220.0440.74999.9
2.21-2.533.90.0445260.9970.0240.0471.069100
2.53-3.193.80.05145900.9940.030.061.28799.9
3.19-253.60.02247970.9990.0140.0261.25699.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YVK

5yvk


Resolution: 1.48→24.12 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.527 / SU ML: 0.026 / SU R Cruickshank DPI: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.045
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1403 2170 4.8 %RANDOM
Rwork0.1085 ---
obs0.11 42745 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.8 Å2 / Biso mean: 18.962 Å2 / Biso min: 10.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 1.48→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 19 331 1886
Biso mean--14.14 35.27 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131629
X-RAY DIFFRACTIONr_bond_other_d00.0171446
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.6692240
X-RAY DIFFRACTIONr_angle_other_deg1.3361.593381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2915215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7124.4379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92615242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.905155
X-RAY DIFFRACTIONr_chiral_restr0.0650.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.021868
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02333
X-RAY DIFFRACTIONr_rigid_bond_restr5.64333075
LS refinement shellResolution: 1.481→1.519 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 130 -
Rwork0.158 3035 -
all-3165 -
obs--97.72 %

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