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- PDB-7kqt: A 1.84-A resolution crystal structure of heme-dependent L-tyrosin... -

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Basic information

Entry
Database: PDB / ID: 7kqt
TitleA 1.84-A resolution crystal structure of heme-dependent L-tyrosine hydroxylase in complex with 3-fluoro-L-tyrosine and cyanide
ComponentsHeme-dependent L-tyrosine hydroxylase
KeywordsOXIDOREDUCTASE / heme-binding enzyme / L-tyrosine hydroxylase
Function / homologyCYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / 3-FLUOROTYROSINE
Function and homology information
Biological speciesStreptomyces sclerotialus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.835 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)71,0529
Polymers69,2462
Non-polymers1,8067
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-54 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.375, 129.446, 48.401
Angle α, β, γ (deg.)90.000, 94.290, 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, 311 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-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
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 42.45 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.835→50 Å / Num. obs: 49481 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.87 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.056 / Rrim(I) all: 0.146 / Χ2: 0.981 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.84-1.876.40.94824720.8270.4071.0340.4799.4
1.87-1.916.50.91725140.7990.3880.9970.59799.1
1.91-1.946.50.78524410.8180.3330.8550.80399.1
1.94-1.986.60.63525000.8950.2670.690.58899
1.98-2.036.60.52224640.9250.2190.5670.55499
2.03-2.076.50.52324730.9110.2250.5710.79698.5
2.07-2.126.50.40524500.9220.1740.4420.7498.1
2.12-2.186.10.32123520.9610.1390.3510.70693.9
2.18-2.256.60.30724390.9590.1310.3350.83797.8
2.25-2.326.80.28725010.9590.120.3111.05499.5
2.32-2.46.80.23525060.9720.0990.2550.9599.5
2.4-2.56.80.20924910.9810.0870.2270.97499.4
2.5-2.616.80.1924690.9820.0790.2061.00399.3
2.61-2.756.60.17524700.9820.0740.191.21598.4
2.75-2.926.50.14824140.9840.0630.1611.16696.1
2.92-3.157.10.13725120.9870.0560.1481.29799.5
3.15-3.466.90.12325100.9860.0510.1331.45599.6
3.46-3.966.70.10724940.990.0450.1171.59698.8
3.96-4.996.80.09224650.9920.0380.0991.49298.1
4.99-506.90.08325440.9950.0330.0891.15299.1

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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: 1.835→48.266 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 2003 4.06 %
Rwork0.2029 47384 -
obs0.2048 49387 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.81 Å2 / Biso mean: 43.039 Å2 / Biso min: 15.84 Å2
Refinement stepCycle: final / Resolution: 1.835→48.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 154 304 5130
Biso mean--42.39 48.98 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074971
X-RAY DIFFRACTIONf_angle_d0.8836800
X-RAY DIFFRACTIONf_chiral_restr0.048723
X-RAY DIFFRACTIONf_plane_restr0.006884
X-RAY DIFFRACTIONf_dihedral_angle_d19.0072901
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.835-1.88090.41211390.3729290285
1.8809-1.93170.41111210.3281346699
1.9317-1.98860.3271500.2874341899
1.9886-2.05280.33421590.2625341199
2.0528-2.12610.30911250.2474341298
2.1261-2.21130.26781490.2191324894
2.2113-2.31190.25381300.2057346899
2.3119-2.43380.26591590.2021342999
2.4338-2.58630.26331390.2016345499
2.5863-2.78590.27611440.205339697
2.7859-3.06620.26381430.2043340598
3.0662-3.50980.23821490.18613452100
3.5098-4.42150.18061420.1652343198
4.4215-48.2660.22461540.1862349299
Refinement TLS params.Method: refined / Origin x: 18.5993 Å / Origin y: 1.3537 Å / Origin z: 13.1792 Å
111213212223313233
T0.1452 Å20.0029 Å2-0.0109 Å2-0.2156 Å2-0.0249 Å2--0.1946 Å2
L0.4565 °2-0.1804 °2-0.17 °2-1.8455 °2-0.5122 °2--1.4878 °2
S0.0397 Å °0.0075 Å °0.017 Å °-0.1782 Å °-0.0432 Å °-0.0024 Å °-0.1055 Å °-0.0859 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 403
2X-RAY DIFFRACTION1allB6 - 403
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 315

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