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- PDB-7yvv: AcmP1, R-4-hydroxymandelate synthase -

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Basic information

Entry
Database: PDB / ID: 7yvv
TitleAcmP1, R-4-hydroxymandelate synthase
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsBIOSYNTHETIC PROTEIN / Fe (II)-dependent dioxygenase / R-Enantioselectivity
Function / homology
Function and homology information


aromatic amino acid metabolic process / 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / metal ion binding
Similarity search - Function
Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal / 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
: / ISOPROPYL ALCOHOL / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesAmycolatopsis sp. Hca4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, B. / Ge, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Characterization of AcmP1 as the native R-4-hydroxymandelate synthase from biosynthetic pathway of Amycolamycins
Authors: Zhang, B. / Ge, H.M.
History
DepositionAug 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5166
Polymers40,2691
Non-polymers2475
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.130, 71.130, 56.281
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase / AcmP1 / R-4-hydroxymandelate synthase


Mass: 40268.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sp. Hca4 (bacteria) / Gene: hppD, HUT10_16010
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A7H8HIR4, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 77.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.33
ReflectionResolution: 2.1→61.6 Å / Num. obs: 18285 / % possible obs: 98.3 % / Redundancy: 4.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.087 / Rrim(I) all: 0.192 / Net I/σ(I): 6.9 / Num. measured all: 85544 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.164.70.938726015420.3920.4771.0551.897.8
8.91-61.64.50.06510792390.9810.0320.07316.597.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R5V

2r5v


Resolution: 2.1→61.6 Å / Cross valid method: THROUGHOUT / σ(F): 84.32 / Phase error: 27.38 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1973 1842 10.08 %
Rwork0.1485 16446 -
obs0.1566 18281 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.28 Å2 / Biso mean: 25.5535 Å2 / Biso min: 4.86 Å2
Refinement stepCycle: final / Resolution: 2.1→61.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 27 197 2804
Biso mean--30.76 33.15 -
Num. residues----335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.25441450.22611301144688
2.16-2.220.21541370.20421264140189
2.22-2.290.25691420.20081247138987
2.29-2.370.27941340.20881261139588
2.37-2.470.23451490.18081254140388
2.47-2.580.19351420.17491283142589
2.58-2.720.26551520.17331259141188
2.72-2.890.21171360.16881249138588
2.89-3.110.21881340.15291251138588
3.11-3.420.20011360.14241282141890
3.42-3.920.17271420.12751273141589
3.92-4.940.15661460.10991270141689
4.95-61.60.15711400.12861252139288
Refinement TLS params.Method: refined / Origin x: 10.019 Å / Origin y: 20.4105 Å / Origin z: 0.9351 Å
111213212223313233
T0.1683 Å20.0008 Å2-0.0136 Å2-0.1396 Å2-0.0049 Å2--0.109 Å2
L0.798 °2-0.1175 °20.0457 °2-0.5791 °20.1007 °2--1.0283 °2
S0.0091 Å °0.0198 Å °-0.1028 Å °-0.0302 Å °0.0157 Å °0.0523 Å °0.0658 Å °0.0482 Å °-0.0366 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 402
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 197

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