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- PDB-5c3r: Crystal structure of the full-length Neurospora crassa T7H in com... -

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Basic information

Entry
Database: PDB / ID: 5c3r
TitleCrystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG and 5-hydroxymethyluracil (5hmU)
ComponentsThymine dioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / substrate B / DSBH fold
Function / homology
Function and homology information


small molecule biosynthetic process / dioxygenase activity / metal ion binding
Similarity search - Function
: / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls ...: / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / 5-HYDROXYMETHYL URACIL / NICKEL (II) ION / Thymine dioxygenase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsLi, W. / Zhang, T. / Ding, J.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2011CB966301 China
Ministry of Science and Technology of China2013CB910404 China
National Natural Science Foundation of China31221001 China
Chinese Academy of SciencesXDB08010302 China
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi
Authors: Li, W. / Zhang, T. / Ding, J.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _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: Thymine dioxygenase
B: Thymine dioxygenase
C: Thymine dioxygenase
D: Thymine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,34729
Polymers154,1534
Non-polymers2,19425
Water10,034557
1
A: Thymine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,25810
Polymers38,5381
Non-polymers7199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-7 kcal/mol
Surface area16230 Å2
MethodPISA
2
B: Thymine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0096
Polymers38,5381
Non-polymers4715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area14430 Å2
MethodPISA
3
C: Thymine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0096
Polymers38,5381
Non-polymers4715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area14450 Å2
MethodPISA
4
D: Thymine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0717
Polymers38,5381
Non-polymers5336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.817, 155.775, 75.992
Angle α, β, γ (deg.)90.000, 91.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thymine dioxygenase


Mass: 38538.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: NCU06416 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: Q7RYZ9

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Non-polymers , 5 types, 582 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-HMU / 5-HYDROXYMETHYL URACIL / 5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 142.113 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6N2O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS-TRIS, 25%(W/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 53781 / % possible obs: 98.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.046 / Rrim(I) all: 0.083 / Χ2: 1.409 / Net I/av σ(I): 19.3 / Net I/σ(I): 15.3 / Num. measured all: 166072
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.433.10.12610.254270.9730.0840.1521.11599.4
2.43-2.533.10.10954230.9770.0730.1321.17699.1
2.53-2.653.10.153670.980.0680.1211.21199.1
2.65-2.793.10.08553970.9850.0570.1021.38599
2.79-2.963.10.07453980.9880.0490.0891.57798.6
2.96-3.193.10.06453640.990.0430.0781.81898.2
3.19-3.513.10.0653670.990.040.0731.20998.3
3.51-4.023.10.06153770.990.040.0731.34297.9
4.02-5.063.10.07253410.9870.0470.0871.80897.4
5.06-5030.05853200.9910.0390.071.44795.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3O

5c3o


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.755 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 2689 5 %RANDOM
Rwork0.1805 ---
obs0.1826 51062 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.21 Å2 / Biso mean: 30.573 Å2 / Biso min: 9.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20.26 Å2
2---0.37 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10140 0 136 557 10833
Biso mean--35.89 32.66 -
Num. residues----1282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01910510
X-RAY DIFFRACTIONr_bond_other_d00.029868
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.96414226
X-RAY DIFFRACTIONr_angle_other_deg3.57322785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5651276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40324.684506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.326151721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0311552
X-RAY DIFFRACTIONr_chiral_restr0.0570.21515
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111940
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022384
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 175 -
Rwork0.192 3779 -
all-3954 -
obs--98.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9329-0.14680.01370.68930.00090.71910.0344-0.08780.02560.0477-0.0146-0.01640.0320.0057-0.01990.01010.00140.00590.02310.01030.03524.408419.471933.0038
20.7434-0.13580.20440.6686-0.06731.09730.0480.12450.0693-0.0561-0.02070.02530.09570.0473-0.02730.01910.02440.01320.05940.04820.0471-5.312921.3977-3.4598
30.939-0.3712-0.57561.17540.41941.51590.08340.06080.0819-0.1733-0.0299-0.0955-0.2088-0.1212-0.05350.04430.01690.00260.0116-0.00170.0761-15.412958.166817.6782
40.86680.0238-0.10730.6353-0.01591.1675-0.0544-0.0934-0.02970.16990.01520.03270.0264-0.09350.03910.05140.01150.00640.0267-0.0110.0252-23.784855.3556-21.9962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 332
2X-RAY DIFFRACTION2B1 - 332
3X-RAY DIFFRACTION3C1 - 332
4X-RAY DIFFRACTION4D3 - 331

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