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- PDB-7kqr: A 1.89-A resolution substrate-bound crystal structure of heme-dep... -

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Basic information

Entry
Database: PDB / ID: 7kqr
TitleA 1.89-A resolution substrate-bound crystal structure of heme-dependent tyrosine hydroxylase from S. sclerotialus
ComponentsHeme-dependent L-tyrosine hydroxylase
KeywordsOXIDOREDUCTASE / heme-binding enzyme / L-tyrosine hydroxylase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / TYROSINE
Function and homology information
Biological speciesStreptomyces sclerotialus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsWang, Y. / Shin, 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 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)71,2959
Polymers69,2462
Non-polymers2,0497
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-50 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.707, 129.781, 48.440
Angle α, β, γ (deg.)90.000, 93.870, 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, 431 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-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
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 6M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 46307 / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.076 / Rrim(I) all: 0.145 / Χ2: 0.842 / Net I/σ(I): 3.5 / Num. measured all: 161341
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.89-1.923.30.96222680.5660.6191.1480.7797.8
1.92-1.963.10.82522480.5560.5520.9970.7996.7
1.96-23.20.66723050.6680.4420.8040.77397.6
2-2.043.60.64522900.7360.3940.7580.79599.7
2.04-2.083.60.53323310.7770.3250.6250.78299.1
2.08-2.133.60.44723260.8360.2740.5250.79499.4
2.13-2.183.60.3723170.8790.2260.4340.80899.4
2.18-2.243.60.32923220.9080.2030.3870.82699.7
2.24-2.313.60.29123510.9260.1790.3420.81899.6
2.31-2.383.60.24323070.9440.150.2860.81499.4
2.38-2.473.50.21922950.9520.1360.2580.82699.6
2.47-2.573.50.20123350.9550.1270.2380.82399.4
2.57-2.683.40.17223350.9510.1090.2040.85199
2.68-2.8230.13822470.9680.0930.1670.85795.9
2.82-33.60.13223180.9770.0810.1560.88699.4
3-3.233.70.10723320.9850.0650.1250.87399.8
3.23-3.563.70.08723170.9860.0530.1020.93199.3
3.56-4.073.60.07423590.9870.0450.0871.03199.4
4.07-5.133.30.05723320.9920.0370.0680.88599.6
5.13-503.60.05823720.9940.0350.0680.88498.8

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-substituted

Resolution: 1.89→48.33 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 2025 4.38 %
Rwork0.1661 44234 -
obs0.1679 46259 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.89 Å2 / Biso mean: 29.6135 Å2 / Biso min: 11.34 Å2
Refinement stepCycle: final / Resolution: 1.89→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 142 424 5247
Biso mean--29.02 36.28 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074985
X-RAY DIFFRACTIONf_angle_d0.8996827
X-RAY DIFFRACTIONf_dihedral_angle_d26.4191825
X-RAY DIFFRACTIONf_chiral_restr0.047725
X-RAY DIFFRACTIONf_plane_restr0.005888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.940.3431330.29053015314895
1.94-1.990.26791480.25843090323897
1.99-2.050.28311520.224631623314100
2.05-2.110.26641340.20763184331899
2.11-2.190.23131510.19083188333999
2.19-2.280.23991410.179531793320100
2.28-2.380.23151410.170631833324100
2.38-2.510.2031510.17173180333199
2.51-2.660.22211460.16793160330699
2.66-2.870.21471530.16243075322897
2.87-3.160.22991440.165732163360100
3.16-3.620.15291430.14733173331699
3.62-4.550.16991450.12743191333699
4.56-48.330.18331430.15243238338199

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