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- PDB-2rdn: Crystal Structure of PtlH with AKG and ent-1PL bound -

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Basic information

Entry
Database: PDB / ID: 2rdn
TitleCrystal Structure of PtlH with AKG and ent-1PL bound
Components1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase
KeywordsOXIDOREDUCTASE / double stranded barrel helix / dioxygenase
Function / homology
Function and homology information


1-deoxypentalenic acid 11beta-hydroxylase / lactone biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / antibiotic biosynthetic process / iron ion binding
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-1PL / 2-OXOGLUTARIC ACID / : / 1-deoxypentalenic acid 11-beta-hydroxylase
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsYou, Z. / Omura, S. / Ikeda, H. / Cane, D.E. / Jogl, G.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of the Non-heme Iron Dioxygenase PtlH in Pentalenolactone Biosynthesis.
Authors: You, Z. / Omura, S. / Ikeda, H. / Cane, D.E. / Jogl, G.
History
DepositionSep 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0736
Polymers32,5891
Non-polymers4855
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.499, 70.106, 48.725
Angle α, β, γ (deg.)90.000, 92.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase


Mass: 32588.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: ptlH / Plasmid: pET28e / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q82IZ1

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Non-polymers , 5 types, 535 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-1PL / (1S,3aS,5aR,8aS)-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylic acid


Mass: 234.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 282 K / Method: sitting drop / pH: 8.5
Details: 100mM Tris, 200mM MgCl2, 20% PEG 3350, pH 8.5, sitting drop, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: ADSC / Detector: CCD / Date: Nov 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 63775 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Χ2: 1.063 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.35-1.43.10.446126321.058199.5
1.4-1.453.10.346126141.059199.7
1.45-1.523.10.256126231.067199.8
1.52-1.63.10.185126541.092199.9
1.6-1.73.10.138126531.1151100
1.7-1.833.20.093127001.0991100
1.83-2.023.20.061126751.0821100
2.02-2.313.20.043126791.03199.9
2.31-2.913.20.034125601.015199.3
2.91-303.30.024122981.015197.1

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se11.8550.130.5020.0560.598
2Se13.4370.2420.3750.2320.669
3Se12.4790.7120.9860.160.589
4Se15.0380.3960.430.4150.67
5Se14.6440.2830.4590.320.639
6Se14.7760.4280.1640.0660.494
7Se26.7790.2240.5030.3430.615
8Se12.5150.7450.450.010.437
9Se45.2440.3070.5550.3740.815
Phasing dmFOM : 0.68 / FOM acentric: 0.68 / FOM centric: 0.64 / Reflection: 61937 / Reflection acentric: 60386 / Reflection centric: 1551
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.9-28.4460.970.970.926962499197
2.4-3.90.930.940.884348118316
1.9-2.40.860.870.741066810371297
1.7-1.90.740.740.561066210427235
1.4-1.70.560.560.471849818169329
1.4-1.40.390.390.331097910802177

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.12phasing
RESOLVE2.12phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.484 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3226 5.1 %RANDOM
Rwork0.172 ---
obs0.173 63775 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.02 Å2
2---0.2 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 30 530 2761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212317
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9563154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80323.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5715366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4611518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021822
X-RAY DIFFRACTIONr_nbd_refined0.20.21252
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2522
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.246
X-RAY DIFFRACTIONr_mcbond_it0.6441.51419
X-RAY DIFFRACTIONr_mcangle_it1.04222258
X-RAY DIFFRACTIONr_scbond_it1.6693993
X-RAY DIFFRACTIONr_scangle_it2.3994.5896
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 245 -
Rwork0.216 4430 -
all-4675 -
obs--99.47 %
Refinement TLS params.Method: refined / Origin x: 13.3223 Å / Origin y: 31.1788 Å / Origin z: 3.8516 Å
111213212223313233
T-0.0138 Å20.0031 Å20.0005 Å2--0.0112 Å2-0.0017 Å2---0.0089 Å2
L0.1655 °2-0.0672 °20.0148 °2-0.3236 °20.0933 °2--0.2514 °2
S0.0063 Å °0.0061 Å °-0.0208 Å °0.0147 Å °-0.0088 Å °0.0082 Å °-0.0171 Å °-0.0175 Å °0.0025 Å °

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