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- PDB-5t2k: Geobacillus stearothermophilus HemQ with Manganese-Coproporphyrin III -

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Basic information

Entry
Database: PDB / ID: 5t2k
TitleGeobacillus stearothermophilus HemQ with Manganese-Coproporphyrin III
ComponentsPutative heme-dependent peroxidase GT50_08830
KeywordsOXIDOREDUCTASE / HemQ / Coproporphyrin III / Decarboxylation
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / heme biosynthetic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Apc35880; domain 1 / Coproheme decarboxylase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-76R / Coproheme decarboxylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus 10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGauss, G.H. / Celis, A.I. / Dubois, J.L. / Peters, J.W.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ).
Authors: Celis, A.I. / Gauss, G.H. / Streit, B.R. / Shisler, K. / Moraski, G.C. / Rodgers, K.R. / Lukat-Rodgers, G.S. / Peters, J.W. / DuBois, J.L.
History
DepositionAug 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: Putative heme-dependent peroxidase GT50_08830
B: Putative heme-dependent peroxidase GT50_08830
C: Putative heme-dependent peroxidase GT50_08830
D: Putative heme-dependent peroxidase GT50_08830
E: Putative heme-dependent peroxidase GT50_08830
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,62610
Polymers144,0885
Non-polymers3,5385
Water24,7351373
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17280 Å2
ΔGint-44 kcal/mol
Surface area44580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.016, 93.458, 132.543
Angle α, β, γ (deg.)90.00, 105.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative heme-dependent peroxidase GT50_08830 / UPF0447 protein GT50_08830


Mass: 28817.609 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus 10 (bacteria)
Gene: GT50_08830 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K2H9D8, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical
ChemComp-76R / [3,3',3'',3'''-(3,8,13,17-tetramethylporphyrin-2,7,12,18-tetrayl-kappa~4~N~21~,N~22~,N~23~,N~24~)tetra(propanoato)(2-)]manganese / Manganese-Coproporphyrin III


Mass: 707.631 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H36MnN4O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1373 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.05 M cadmium sulfate, 0.8-1.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→38.4 Å / Num. obs: 142652 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.824 / % possible all: 86.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T0T

1t0t


Resolution: 1.8→38.4 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.28
RfactorNum. reflection% reflection
Rfree0.1761 7153 5.02 %
Rwork0.1536 --
obs0.1548 142519 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9869 0 245 1373 11487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910711
X-RAY DIFFRACTIONf_angle_d1.69614629
X-RAY DIFFRACTIONf_dihedral_angle_d10.1866318
X-RAY DIFFRACTIONf_chiral_restr0.0541512
X-RAY DIFFRACTIONf_plane_restr0.0071869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7958-1.81620.31012120.26743643X-RAY DIFFRACTION81
1.8162-1.83760.29122480.23864549X-RAY DIFFRACTION100
1.8376-1.860.2582310.22094482X-RAY DIFFRACTION100
1.86-1.88350.22862350.20364536X-RAY DIFFRACTION100
1.8835-1.90830.22382760.19664510X-RAY DIFFRACTION100
1.9083-1.93440.22592470.19384484X-RAY DIFFRACTION100
1.9344-1.96210.22562350.18784537X-RAY DIFFRACTION100
1.9621-1.99130.2192210.18264523X-RAY DIFFRACTION100
1.9913-2.02250.19842390.17394513X-RAY DIFFRACTION100
2.0225-2.05560.19962310.17974521X-RAY DIFFRACTION100
2.0556-2.09110.21732240.17284532X-RAY DIFFRACTION100
2.0911-2.12910.1952170.16744559X-RAY DIFFRACTION100
2.1291-2.170.17672580.1614528X-RAY DIFFRACTION100
2.17-2.21430.19352200.16054544X-RAY DIFFRACTION100
2.2143-2.26250.19742450.16084508X-RAY DIFFRACTION100
2.2625-2.31510.19992530.15694550X-RAY DIFFRACTION100
2.3151-2.3730.19082360.15014551X-RAY DIFFRACTION100
2.373-2.43710.20512300.154545X-RAY DIFFRACTION100
2.4371-2.50880.18462340.15584503X-RAY DIFFRACTION100
2.5088-2.58980.17292340.14614578X-RAY DIFFRACTION100
2.5898-2.68230.16242420.1454560X-RAY DIFFRACTION100
2.6823-2.78970.18752250.15254529X-RAY DIFFRACTION100
2.7897-2.91660.16092310.14664549X-RAY DIFFRACTION100
2.9166-3.07030.17232360.14894557X-RAY DIFFRACTION100
3.0703-3.26260.16662380.14814558X-RAY DIFFRACTION100
3.2626-3.51430.14322780.13974543X-RAY DIFFRACTION100
3.5143-3.86770.15342700.13554542X-RAY DIFFRACTION100
3.8677-4.42670.13142350.12294572X-RAY DIFFRACTION100
4.4267-5.57440.13462140.12484621X-RAY DIFFRACTION100
5.5744-38.41060.18252580.16614639X-RAY DIFFRACTION99

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