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- PDB-7rmu: Structure of Thermomonospora curvata heme-containing DyP-type per... -

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Basic information

Entry
Database: PDB / ID: 7rmu
TitleStructure of Thermomonospora curvata heme-containing DyP-type peroxidase with a modified axial ligand
ComponentsDyP-type Peroxidase
KeywordsOXIDOREDUCTASE / Dye-decolorizing peroxidase / heme / unnatural amino acid
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase family
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKhadka, S. / Li, P. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: To Be Published
Title: Structure of Thermomonospora curvata heme-containing DyP-type peroxidase with a modified axial ligand
Authors: Khadka, S. / Geisbrecht, B. / Li, P.
History
DepositionJul 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DyP-type Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9809
Polymers43,6911
Non-polymers1,2898
Water2,414134
1
A: DyP-type Peroxidase
hetero molecules

A: DyP-type Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,96018
Polymers87,3822
Non-polymers2,57816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area9160 Å2
ΔGint-194 kcal/mol
Surface area28490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.698, 87.698, 107.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-643-

HOH

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Components

#1: Protein DyP-type Peroxidase


Mass: 43691.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Gene: Tcur_2987 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D1A807
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.01 Å3/Da / Density % sol: 59.13 % / Description: rod-like
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic (pH 5.6), 0.5 M ammonium sulfate, 1.0 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 27294 / % possible obs: 97.8 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.017 / Rrim(I) all: 0.08 / Χ2: 1.009 / Net I/σ(I): 10.5 / Num. measured all: 577899
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1812.20.81622370.410.2240.851.04381.5
2.18-2.2616.60.81426680.8470.2010.841.03196.3
2.26-2.3721.50.75227830.9450.1650.771.038100
2.37-2.4922.90.54427610.9720.1160.5560.987100
2.49-2.6522.90.35827680.9880.0760.3661.016100
2.65-2.8522.90.21927720.9950.0460.2240.99100
2.85-3.1422.90.1327960.9980.0280.1330.995100
3.14-3.5922.90.07927940.9990.0170.0810.964100
3.59-4.5222.80.05328140.9990.0110.0540.966100
4.52-5022.20.037290110.0080.0381.089100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JXU

5jxu


Resolution: 2.1→43.85 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 1994 7.32 %
Rwork0.1704 25250 -
obs0.1733 27244 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.5 Å2 / Biso mean: 57.6199 Å2 / Biso min: 29.07 Å2
Refinement stepCycle: final / Resolution: 2.1→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 78 134 3011
Biso mean--79.66 55.3 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072946
X-RAY DIFFRACTIONf_angle_d0.9154021
X-RAY DIFFRACTIONf_dihedral_angle_d13.8731082
X-RAY DIFFRACTIONf_chiral_restr0.047414
X-RAY DIFFRACTIONf_plane_restr0.005534
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 (%)
2.1-2.150.30591060.24911413151978
2.15-2.210.29561310.23491692182392
2.21-2.280.25631430.21621801194499
2.28-2.350.25411470.214818331980100
2.35-2.430.26281440.202118371981100
2.43-2.530.27231460.199818341980100
2.53-2.650.26491410.197618301971100
2.65-2.790.24931500.204518401990100
2.79-2.960.24581460.20918371983100
2.96-3.190.26321460.207118431989100
3.19-3.510.21951490.187718562005100
3.51-4.020.22251470.156818421989100
4.02-5.060.14391430.125318712014100
5.06-43.850.16971550.143519212076100
Refinement TLS params.Method: refined / Origin x: 11.7788 Å / Origin y: 24.7881 Å / Origin z: 6.3996 Å
111213212223313233
T0.3055 Å20.0066 Å2-0.055 Å2-0.5498 Å2-0.1477 Å2--0.4121 Å2
L1.406 °2-0.137 °20.3449 °2-1.4967 °2-0.3868 °2--1.5842 °2
S-0.1843 Å °-0.2386 Å °0.1893 Å °0.0483 Å °-0.0507 Å °0.247 Å °-0.0921 Å °-0.4926 Å °0.2176 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA43 - 501
2X-RAY DIFFRACTION1allB1 - 7
3X-RAY DIFFRACTION1allS1 - 134

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