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- PDB-6e1c: Crystal structure of a MauG-like protein associated with microbia... -

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Basic information

Entry
Database: PDB / ID: 6e1c
TitleCrystal structure of a MauG-like protein associated with microbial copper homeostasis
ComponentsDi-heme enzyme
KeywordsMETAL BINDING PROTEIN / Di-heme cytochrome c peroxidase.
Function / homology
Function and homology information


electron transfer activity / periplasmic space / heme binding / metal ion binding
Similarity search - Function
Di-heme enzyme, MXAN0977 / Di-c-type haem protein, MauG/cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Di-heme enzyme
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.617 Å
AuthorsDassama, L.M.K. / Rosenzweig, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM110934 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118035 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: MbnH is a diheme MauG-like protein associated with microbial copper homeostasis.
Authors: Kenney, G.E. / Dassama, L.M.K. / Manesis, A.C. / Ross, M.O. / Chen, S. / Hoffman, B.M. / Rosenzweig, A.C.
History
DepositionJul 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Di-heme enzyme
B: Di-heme enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9988
Polymers85,4442
Non-polymers2,5546
Water93752
1
A: Di-heme enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9994
Polymers42,7221
Non-polymers1,2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Di-heme enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9994
Polymers42,7221
Non-polymers1,2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.557, 85.757, 133.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Di-heme enzyme


Mass: 42721.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_07135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2CY72
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PPG 400, Bis-Tris

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.722003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722003 Å / Relative weight: 1
ReflectionResolution: 2.617→42.88 Å / Num. obs: 24860 / % possible obs: 97.59 % / Redundancy: 10.6 % / Biso Wilson estimate: 26.17 Å2 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.035 / Rrim(I) all: 0.152 / Net I/σ(I): 21.26
Reflection shellResolution: 2.617→2.69 Å / Rmerge(I) obs: 0.846 / Rpim(I) all: 0.202 / Rrim(I) all: 0.871

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.617→42.879 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.37 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 1998 8.04 %RANDOM
Rwork0.1981 22858 --
obs0.2046 24856 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.43 Å2 / Biso mean: 35.8157 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.617→42.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 174 52 5457
Biso mean--15.55 17.69 -
Num. residues----673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135554
X-RAY DIFFRACTIONf_angle_d1.6647597
X-RAY DIFFRACTIONf_chiral_restr0.067763
X-RAY DIFFRACTIONf_plane_restr0.01991
X-RAY DIFFRACTIONf_dihedral_angle_d17.1283206
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 (%)
2.6171-2.68260.3691190.25851358147783
2.6826-2.75510.37531420.25961620176298
2.7551-2.83620.33431390.25021588172798
2.8362-2.92770.35221420.24431636177899
2.9277-3.03230.34241420.22961617175998
3.0323-3.15370.30651430.23211624176798
3.1537-3.29720.29991430.2191656179999
3.2972-3.47090.34221450.21516511796100
3.4709-3.68830.25311430.194816501793100
3.6883-3.97280.26371470.17591668181599
3.9728-4.37230.21071450.15171651179699
4.3723-5.00420.2151470.14731687183499
5.0042-6.30150.23111440.16991647179196
6.3015-42.88420.24591570.193118051962100

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