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- PDB-7fc0: Reconstitution of MbnABC complex from Rugamonas rubra ATCC-43154 ... -

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Basic information

Entry
Database: PDB / ID: 7fc0
TitleReconstitution of MbnABC complex from Rugamonas rubra ATCC-43154 (GroupIII)
Components
  • (Methanobactin biosynthesis cassette protein ...) x 3
  • RrMbnA precosur peptide
KeywordsMETAL BINDING PROTEIN / Fe binding protein / MbnABC complex / Methanobactin.
Function / homology
Function and homology information


Conserved hypothetical protein CHP04061, AZL007950 / Methanobactin biosynthesis cassette protein MbnB / Uncharacterised protein family UPF0276 / RiPP precursor modification enzyme MbnB/TglH/ChrH / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Methanobactin biosynthesis cassette protein MbnC / Methanobactin biosynthesis cassette protein MbnB
Similarity search - Component
Biological speciesRugamonas rubra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.643 Å
AuthorsChao, D. / Zhaolin, L. / Shoujie, L. / Li, Z. / Dan, Z. / Ying, J. / Wei, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res. / Year: 2022
Title: Crystal structure and catalytic mechanism of the MbnBC holoenzyme required for methanobactin biosynthesis.
Authors: Dou, C. / Long, Z. / Li, S. / Zhou, D. / Jin, Y. / Zhang, L. / Zhang, X. / Zheng, Y. / Li, L. / Zhu, X. / Liu, Z. / He, S. / Yan, W. / Yang, L. / Xiong, J. / Fu, X. / Qi, S. / Ren, H. / ...Authors: Dou, C. / Long, Z. / Li, S. / Zhou, D. / Jin, Y. / Zhang, L. / Zhang, X. / Zheng, Y. / Li, L. / Zhu, X. / Liu, Z. / He, S. / Yan, W. / Yang, L. / Xiong, J. / Fu, X. / Qi, S. / Ren, H. / Chen, S. / Dai, L. / Wang, B. / Cheng, W.
History
DepositionJul 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: RrMbnA precosur peptide
E: Methanobactin biosynthesis cassette protein MbnB
B: Methanobactin biosynthesis cassette protein MbnB
F: Methanobactin biosynthesis cassette protein MbnC
C: Methanobactin biosynthesis cassette protein MbnC
D: RrMbnA precosur peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,68612
Polymers109,3516
Non-polymers3356
Water1,928107
1
A: RrMbnA precosur peptide
B: Methanobactin biosynthesis cassette protein MbnB
C: Methanobactin biosynthesis cassette protein MbnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8146
Polymers54,6473
Non-polymers1683
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-84 kcal/mol
Surface area19100 Å2
MethodPISA
2
E: Methanobactin biosynthesis cassette protein MbnB
F: Methanobactin biosynthesis cassette protein MbnC
D: RrMbnA precosur peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8726
Polymers54,7043
Non-polymers1683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-84 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.968, 173.968, 61.185
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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Protein/peptide , 1 types, 2 molecules AD

#1: Protein/peptide RrMbnA precosur peptide


Mass: 3057.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rugamonas rubra (bacteria) / Production host: Escherichia coli (E. coli)

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Methanobactin biosynthesis cassette protein ... , 3 types, 4 molecules EBFC

#2: Protein Methanobactin biosynthesis cassette protein MbnB


Mass: 29616.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rugamonas rubra (bacteria) / Gene: SAMN02982985_00539 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I4IFL0
#3: Protein Methanobactin biosynthesis cassette protein MbnB


Mass: 29559.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rugamonas rubra (bacteria) / Gene: SAMN02982985_00539 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I4IFL0
#4: Protein Methanobactin biosynthesis cassette protein MbnC


Mass: 22030.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rugamonas rubra (bacteria) / Gene: SAMN02982985_00538 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I4IFH0

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Non-polymers , 2 types, 113 molecules

#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.24 Å3/Da / Density % sol: 70.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 12% PEG20000, 160 mM MES pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.643→61.51 Å / Num. obs: 54150 / % possible obs: 99.8 % / Redundancy: 13 % / Biso Wilson estimate: 67.94 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.21 / Net I/σ(I): 6.46
Reflection shellResolution: 2.643→2.738 Å / Num. unique obs: 5328 / CC1/2: 0.564

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DZ9

7dz9


Resolution: 2.643→61.51 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 5123 4.89 %
Rwork0.178 --
obs0.18 54089 99.78 %
Displacement parametersBiso mean: 91.8 Å2
Refinement stepCycle: LAST / Resolution: 2.643→61.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7602 0 6 107 7715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00877794
X-RAY DIFFRACTIONf_angle_d1.16210587
X-RAY DIFFRACTIONf_chiral_restr0.06721126
X-RAY DIFFRACTIONf_plane_restr0.00711397
X-RAY DIFFRACTIONf_dihedral_angle_d22.65182805
LS refinement shellResolution: 2.643→2.67 Å
RfactorNum. reflection% reflection
Rfree0.4279 --
Rwork0.382 3353 -
obs--100 %

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