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- PDB-5z54: Crystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43... -

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Basic information

Entry
Database: PDB / ID: 5z54
TitleCrystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239 in complex with cyclo-L-Arg-D-Pro
Components12-epi-hapalindole C/U synthase
KeywordsTRANSFERASE / prenyltransferase
Function / homologyChem-0HZ / 12-epi-hapalindole C/U synthase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsHu, X.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement
Authors: Chen, C.C. / Hu, X. / Tang, X. / Yang, Y. / Ko, T.P. / Gao, J. / Zheng, Y. / Huang, J.W. / Yu, Z. / Li, L. / Han, S. / Cai, N. / Zhang, Y. / Liu, W. / Guo, R.T.
History
DepositionJan 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 12-epi-hapalindole C/U synthase
B: 12-epi-hapalindole C/U synthase
C: 12-epi-hapalindole C/U synthase
D: 12-epi-hapalindole C/U synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,57316
Polymers99,2354
Non-polymers1,33812
Water4,125229
1
A: 12-epi-hapalindole C/U synthase
hetero molecules

D: 12-epi-hapalindole C/U synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2878
Polymers49,6182
Non-polymers6696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
Buried area1710 Å2
ΔGint-5 kcal/mol
Surface area16510 Å2
MethodPISA
2
B: 12-epi-hapalindole C/U synthase
hetero molecules

C: 12-epi-hapalindole C/U synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2878
Polymers49,6182
Non-polymers6696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area1750 Å2
ΔGint-5 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.557, 113.374, 132.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
12-epi-hapalindole C/U synthase / HpiU5


Mass: 24808.873 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Gene: hpiU5 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A076NBW8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: 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.: 4 / Source method: obtained synthetically / Formula: C11H20N5O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.36 Å3/Da / Density % sol: 47.98 % / Mosaicity: 0.764 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M sodium chloride, 20%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 29, 2017
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→25 Å / Num. obs: 49997 / % possible obs: 99.8 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.024 / Rrim(I) all: 0.091 / Χ2: 0.862 / Net I/σ(I): 7.2 / Num. measured all: 630102
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.28-2.3611.60.49542690.9550.1460.5170.51298.2
2.36-2.4613.50.4543520.980.1250.4670.526100
2.46-2.5714.70.35943700.990.0970.3720.556100
2.57-2.7150.28643690.9920.0760.2960.606100
2.7-2.87150.21443980.9950.0570.2220.654100
2.87-3.0914.90.13543880.9970.0360.140.797100
3.09-3.414.80.09544020.9980.0260.0991.123100
3.4-3.8914.70.06844450.9990.0180.0711.376100
3.89-4.914.40.05444950.9990.0150.0561.364100
4.9-25140.04846810.9990.0130.050.981100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YVK

5yvk


Resolution: 2.16→24.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.965 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23028 2493 5 %RANDOM
Rwork0.18162 ---
obs0.18406 47439 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.001 Å2
Baniso -1Baniso -2Baniso -3
1--4.98 Å2-0 Å20 Å2
2--5.7 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.16→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6144 0 80 229 6453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.6618720
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1575790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22424.5320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35215926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2281520
X-RAY DIFFRACTIONr_chiral_restr0.1060.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7654.5533212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.196.813966
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4144.933216
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.93988.05828252
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.156→2.212 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 138 -
Rwork0.299 2657 -
obs--74.95 %

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