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- PDB-6eci: Structure of the FAD binding protein MSMEG_5243 from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 6eci
TitleStructure of the FAD binding protein MSMEG_5243 from Mycobacterium smegmatis
ComponentsPyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
KeywordsFAD-BINDING PROTEIN / flavin adenine dinucleotide (FAD) binding protein / flavin/deazaflavin dependent oxidoreductase (FDOR)
Function / homologyPyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / FLAVIN-ADENINE DINUCLEOTIDE / Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.69 Å
AuthorsAhmed, F.H. / Antoney, J. / Carr, P.D. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J. Biol. Chem. / Year: 2019
Title: FAD-sequestering proteins protect mycobacteria against hypoxic and oxidative stress.
Authors: Harold, L.K. / Antoney, J. / Ahmed, F.H. / Hards, K. / Carr, P.D. / Rapson, T. / Greening, C. / Jackson, C.J. / Cook, G.M.
History
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
C: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
D: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
E: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
F: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
G: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
H: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
I: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
J: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
K: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
L: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
M: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
N: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
O: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
P: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
Q: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
R: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
S: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
T: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,14138
Polymers293,75220
Non-polymers13,39018
Water6,485360
1
A: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9825
Polymers29,3752
Non-polymers1,6073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-30 kcal/mol
Surface area12270 Å2
MethodPISA
2
C: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
D: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9464
Polymers29,3752
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-26 kcal/mol
Surface area12260 Å2
MethodPISA
3
E: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
F: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9464
Polymers29,3752
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-23 kcal/mol
Surface area12360 Å2
MethodPISA
4
G: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
H: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9464
Polymers29,3752
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-23 kcal/mol
Surface area11490 Å2
MethodPISA
5
I: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
J: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1613
Polymers29,3752
Non-polymers7861
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-15 kcal/mol
Surface area12330 Å2
MethodPISA
6
K: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
L: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1613
Polymers29,3752
Non-polymers7861
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-19 kcal/mol
Surface area12650 Å2
MethodPISA
7
M: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
N: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9464
Polymers29,3752
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-32 kcal/mol
Surface area11950 Å2
MethodPISA
8
O: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
P: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1613
Polymers29,3752
Non-polymers7861
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-21 kcal/mol
Surface area12470 Å2
MethodPISA
9
Q: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
R: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9464
Polymers29,3752
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-21 kcal/mol
Surface area11840 Å2
MethodPISA
10
S: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
T: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9464
Polymers29,3752
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-21 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.268, 186.039, 195.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Mass: 14687.581 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_5105 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I7GF07
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 20% polyethylene glycol 1500, 4% 2-methyl-2,4-pentanediol and 0.1 M citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.69→29.6 Å / Num. obs: 82043 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 38.99 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.084 / Rrim(I) all: 0.231 / Net I/σ(I): 10.5
Reflection shellResolution: 2.69→2.74 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.444 / Num. unique obs: 4447 / CC1/2: 0.551 / Rpim(I) all: 0.565 / Rrim(I) all: 1.552 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FHK

3fhk


Resolution: 2.69→29.599 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.27
RfactorNum. reflection% reflection
Rfree0.2587 4121 5.03 %
Rwork0.2092 --
obs0.2117 81939 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.84 Å2 / Biso mean: 45.8358 Å2 / Biso min: 1.31 Å2
Refinement stepCycle: final / Resolution: 2.69→29.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19180 0 902 362 20444
Biso mean--44.92 34.13 -
Num. residues----2422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.69-2.72170.38771410.310626422783100
2.7217-2.75480.35821620.29126252787100
2.7548-2.78970.33011360.279326572793100
2.7897-2.82630.37831380.275826462784100
2.8263-2.8650.30831430.259726742817100
2.865-2.90590.27981230.248126502773100
2.9059-2.94930.32951580.249626202778100
2.9493-2.99530.34951420.258726622804100
2.9953-3.04440.31841510.251226512802100
3.0444-3.09680.291560.228926712827100
3.0968-3.15310.31551380.224226222760100
3.1531-3.21360.2391510.217826942845100
3.2136-3.27920.27871280.212726482776100
3.2792-3.35040.28051400.211226752815100
3.3504-3.42820.24681390.204126472786100
3.4282-3.51380.27411660.210626622828100
3.5138-3.60860.24921400.21226812821100
3.6086-3.71460.23711380.19326622800100
3.7146-3.83430.27631490.193826882837100
3.8343-3.9710.26281480.192426922840100
3.971-4.12960.23711420.188626632805100
4.1296-4.3170.26211340.182127072841100
4.317-4.54380.22831100.164427232833100
4.5438-4.82740.1821620.164626922854100
4.8274-5.19830.1921250.172227132838100
5.1983-5.7180.22461250.199127592884100
5.718-6.53760.26171350.212927532888100
6.5376-8.20750.23441400.210927922932100
8.2075-29.60070.2061610.21172847300899

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