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- PDB-5mjh: X-ray generated oxyferrous/water mixed complex of DtpA from Strep... -

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Basic information

Entry
Database: PDB / ID: 5mjh
TitleX-ray generated oxyferrous/water mixed complex of DtpA from Streptomyces lividans
ComponentsDye type peroxidase A
KeywordsOXIDOREDUCTASE / peroxidase radiolysis oxygen dye-type
Function / homology
Function and homology information


iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Deferrochelatase / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Deferrochelatase/peroxidase
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMoreno Chicano, T. / Chaplin, A.K. / Worrall, J.A.R. / Strange, R.W. / Hough, M.A.
CitationJournal: IUCrJ / Year: 2017
Title: Photoreduction and validation of haem-ligand intermediate states in protein crystals by in situ single-crystal spectroscopy and diffraction.
Authors: Kekilli, D. / Moreno-Chicano, T. / Chaplin, A.K. / Horrell, S. / Dworkowski, F.S.N. / Worrall, J.A.R. / Strange, R.W. / Hough, M.A.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dye type peroxidase A
B: Dye type peroxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4606
Polymers81,1632
Non-polymers1,2974
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-50 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.782, 70.627, 77.642
Angle α, β, γ (deg.)90.00, 93.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dye type peroxidase A


Mass: 40581.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SLIV_18505 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A076MAJ9
#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
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Crystals were grown by the vapour diffusion hanging drop method using a ferric protein solution at 13 mg/ml equilibrated against a reservoir consisting of 17-24% PEG 3000 and 50-100 mM sodium citrate, pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2015 / Details: mirrors
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→77.53 Å / Num. obs: 112162 / % possible obs: 98.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→77.53 Å / SU B: 2.113 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.092
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 5529 4.9 %RANDOM
Rwork0.221 ---
obs0.222 106599 98.1 %-
Displacement parametersBiso mean: 12.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.15 Å2
2--0.09 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.45→77.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 95 621 6313

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