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- PDB-7kqu: A 1.58-A resolution crystal structure of ferric-hydroperoxo inter... -

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Basic information

Entry
Database: PDB / ID: 7kqu
TitleA 1.58-A resolution crystal structure of ferric-hydroperoxo intermediate of L-tyrosine hydroxylase in complex with 3-fluoro-L-tyrosine
ComponentsHeme-dependent L-tyrosine hydroxylase
KeywordsOXIDOREDUCTASE / heme-binding enzyme / L-tyrosine hydroxylase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / HYDROGEN PEROXIDE / 3-FLUOROTYROSINE
Function and homology information
Biological speciesStreptomyces sclerotialus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.579 Å
AuthorsWang, Y. / Davis, I. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Molecular Rationale for Partitioning between C-H and C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase.
Authors: Wang, Y. / Davis, I. / Shin, I. / Xu, H. / Liu, A.
History
DepositionNov 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Heme-dependent L-tyrosine hydroxylase
B: Heme-dependent L-tyrosine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,27710
Polymers69,2462
Non-polymers2,0318
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-53 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.523, 129.329, 48.380
Angle α, β, γ (deg.)90.000, 94.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Heme-dependent L-tyrosine hydroxylase


Mass: 34623.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sclerotialus (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 573 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-YOF / 3-FLUOROTYROSINE


Type: L-peptide linking / Mass: 199.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10FNO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris (pH 6.1), 0.2 M MgCl2, and 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.579→50 Å / Num. obs: 79437 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.081 / Rrim(I) all: 0.175 / Χ2: 1.097 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.613.50.74940000.6270.4480.8770.31799.9
1.61-1.643.80.69439750.70.3970.8030.32999.9
1.64-1.674.10.66939440.7450.3660.7650.349100
1.67-1.74.30.60739740.7930.3230.6890.367100
1.7-1.744.50.56139370.8240.290.6330.383100
1.74-1.784.80.53439800.7840.270.60.415100
1.78-1.824.90.47139820.8840.2350.5280.462100
1.82-1.8750.41339650.9070.2050.4610.526100
1.87-1.9350.3639850.9230.1770.4010.631100
1.93-1.9950.30739660.9330.1520.3430.762100
1.99-2.0650.27139690.9450.1350.3030.894100
2.06-2.1450.23939440.9480.1190.2671.158100
2.14-2.2450.21439810.9590.1060.2391.339100
2.24-2.3650.20439770.9580.1020.2291.597100
2.36-2.5150.19340160.9590.0970.2161.808100
2.51-2.750.18539720.960.0930.2072.0299.9
2.7-2.9750.17539810.9620.0870.1962.26100
2.97-3.44.80.14539800.9710.0750.1632.19199.9
3.4-4.294.60.11739440.9710.0640.1331.97298.7
4.29-504.70.08839650.9830.0490.1021.32597.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.10.1refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KQR

7kqr


Resolution: 1.579→45.215 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 2014 2.54 %
Rwork0.1565 77378 -
obs0.1573 79392 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.9 Å2 / Biso mean: 30.6631 Å2 / Biso min: 11.59 Å2
Refinement stepCycle: final / Resolution: 1.579→45.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 168 565 5398
Biso mean--30.32 42.48 -
Num. residues----602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065038
X-RAY DIFFRACTIONf_angle_d0.8616899
X-RAY DIFFRACTIONf_chiral_restr0.047731
X-RAY DIFFRACTIONf_plane_restr0.006898
X-RAY DIFFRACTIONf_dihedral_angle_d19.4782954
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5792-1.61870.29661350.2457549999
1.6187-1.66250.23331560.21985517100
1.6625-1.71140.23931260.20945530100
1.7114-1.76660.25361520.19665558100
1.7666-1.82980.2061490.17595481100
1.8298-1.90310.2241400.16355552100
1.9031-1.98970.2021460.16045527100
1.9897-2.09460.19571430.1625539100
2.0946-2.22580.17411410.14975515100
2.2258-2.39760.18771440.15135545100
2.3976-2.63890.20341480.15895544100
2.6389-3.02070.19981450.1575551100
3.0207-3.80540.16061430.1425530100
3.8054-45.2150.16971460.1422549098
Refinement TLS params.Method: refined / Origin x: 62.7614 Å / Origin y: 1.0789 Å / Origin z: 61.5465 Å
111213212223313233
T0.1145 Å20.0025 Å20.001 Å2-0.153 Å2-0.0239 Å2--0.128 Å2
L0.4789 °2-0.1036 °2-0.0926 °2-1.2347 °2-0.3127 °2--0.8078 °2
S0.0358 Å °0.0039 Å °0.0174 Å °-0.0585 Å °-0.0485 Å °0.0044 Å °-0.0473 Å °-0.0887 Å °0.0102 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 307
2X-RAY DIFFRACTION1allB6 - 306
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allE2
5X-RAY DIFFRACTION1allD1 - 2
6X-RAY DIFFRACTION1allS1 - 626
7X-RAY DIFFRACTION1allF1 - 2
8X-RAY DIFFRACTION1allH1

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