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- PDB-7dz9: MbnABC complex -

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Basic information

Entry
Database: PDB / ID: 7dz9
TitleMbnABC complex
Components
  • (MbnA) x 2
  • MbnB
  • MbnC
  • cpMbnB
KeywordsPEPTIDE BINDING PROTEIN / MbnA coordinated with MbnBC
Function / homology
Function and homology information


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
: / Uncharacterized protein / DUF692 domain-containing protein
Similarity search - Component
Biological speciesVibrio caribbeanicus ATCC BAA-2122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChao, D. / Dan, Z. / Yijun, G. / Wei, C.
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
DepositionJan 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MbnB
B: cpMbnB
D: MbnC
E: MbnA
F: MbnA
C: MbnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,90912
Polymers107,5746
Non-polymers3356
Water3,837213
1
A: MbnB
D: MbnC
F: MbnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8836
Polymers53,7153
Non-polymers1683
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-84 kcal/mol
Surface area19230 Å2
MethodPISA
2
B: cpMbnB
E: MbnA
C: MbnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0266
Polymers53,8593
Non-polymers1683
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-87 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.915, 69.065, 82.573
Angle α, β, γ (deg.)90.000, 93.590, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 3 types, 4 molecules ABDC

#1: Protein MbnB


Mass: 29984.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio caribbeanicus ATCC BAA-2122 (bacteria)
Gene: VIBC2010_09967
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E3BK14
#2: Protein cpMbnB


Mass: 29998.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio caribbeanicus ATCC BAA-2122 (bacteria)
Gene: VIBC2010_09967
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E3BK14
#3: Protein MbnC


Mass: 21212.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio caribbeanicus ATCC BAA-2122 (bacteria)
Gene: VIBC2010_09962
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E3BK13

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Protein/peptide , 2 types, 2 molecules EF

#4: Protein/peptide MbnA


Mass: 2648.233 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio caribbeanicus ATCC BAA-2122 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#5: Protein/peptide MbnA


Mass: 2519.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio caribbeanicus ATCC BAA-2122 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 2 types, 219 molecules

#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 2% Tacsimate pH7.0, HEPES pH7.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→43.64 Å / Num. obs: 46642 / % possible obs: 99.36 % / Redundancy: 13.7 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1183 / Net I/σ(I): 18.78
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 4648 / CC1/2: 0.971

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→43.64 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 2084 -
Rwork0.1726 --
obs-46642 99.37 %
Displacement parametersBiso mean: 27.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7562 0 6 213 7781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857738
X-RAY DIFFRACTIONf_angle_d0.938410466
X-RAY DIFFRACTIONf_chiral_restr0.05451157
X-RAY DIFFRACTIONf_plane_restr0.00591335
X-RAY DIFFRACTIONf_dihedral_angle_d17.65012842
LS refinement shellResolution: 2.2→2.279 Å
RfactorNum. reflection% reflection
Rfree0.4078 --
Rwork0.3927 --
obs-4648 99.64 %

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