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- PDB-7kqs: A 1.68-A resolution 3-fluoro-L-tyrosine bound crystal structure o... -

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Basic information

Entry
Database: PDB / ID: 7kqs
TitleA 1.68-A resolution 3-fluoro-L-tyrosine bound crystal structure of heme-dependent tyrosine hydroxylase
ComponentsHeme-dependent L-tyrosine hydroxylase
KeywordsOXIDOREDUCTASE / heme-binding enzyme / L-tyrosine hydroxylase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / 3-FLUOROTYROSINE
Function and homology information
Biological speciesStreptomyces sclerotialus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.677 Å
AuthorsWang, Y. / 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)71,2098
Polymers69,2462
Non-polymers1,9636
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-55 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.526, 129.719, 48.533
Angle α, β, γ (deg.)90.000, 94.190, 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 , 5 types, 399 molecules

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


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 / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
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: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.677→50 Å / Num. obs: 66499 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 23.39 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.056 / Rrim(I) all: 0.124 / Χ2: 1.047 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.713.90.96132550.6350.5391.1060.4398.2
1.71-1.744.10.90332920.6760.51.0350.45499.5
1.74-1.774.30.83633390.7150.4540.9550.4599.9
1.77-1.814.40.72333140.7920.3890.8230.472100
1.81-1.854.50.61833170.810.3270.7010.508100
1.85-1.894.60.51833190.8840.2730.5870.526100
1.89-1.944.60.42233270.9090.2220.4780.577100
1.94-1.994.60.35232910.9330.1830.3980.629100
1.99-2.054.70.29533470.9530.1520.3330.702100
2.05-2.124.70.24733340.9610.1270.2780.764100
2.12-2.194.80.21633210.970.110.2420.898100
2.19-2.284.90.19333310.9760.0970.2171.017100
2.28-2.384.90.18133210.9730.0910.2031.162100
2.38-2.5150.16633480.9810.0830.1861.286100
2.51-2.6750.14833150.9810.0740.1651.477100
2.67-2.8750.1333400.9830.0650.1451.729100
2.87-3.1650.11433390.9850.0580.1281.872100
3.16-3.624.90.08833420.9890.0460.11.926100
3.62-4.5650.0733300.9910.0360.0791.848100
4.56-5050.0633770.9940.0310.0681.48398.9

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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: 1.677→47.399 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 2016 3.03 %
Rwork0.1725 64428 -
obs0.1734 66444 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.65 Å2 / Biso mean: 30.4986 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 1.677→47.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 164 393 5220
Biso mean--29.85 38.6 -
Num. residues----601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065007
X-RAY DIFFRACTIONf_angle_d0.8556862
X-RAY DIFFRACTIONf_chiral_restr0.05729
X-RAY DIFFRACTIONf_plane_restr0.006891
X-RAY DIFFRACTIONf_dihedral_angle_d20.3942943
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6773-1.71920.30971300.2981425393
1.7192-1.76570.31261560.28424617100
1.7657-1.81760.34921450.25674635100
1.8176-1.87630.29431340.22174587100
1.8763-1.94340.25891460.20514648100
1.9434-2.02120.25651400.18774620100
2.0212-2.11320.22141330.18434643100
2.1132-2.22460.19341540.16954582100
2.2246-2.3640.19641440.16724628100
2.364-2.54650.22151410.17184655100
2.5465-2.80270.20351440.17534634100
2.8027-3.20820.21951510.17444649100
3.2082-4.04170.15911490.14574634100
4.0417-47.3990.16831490.1494464399

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