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- PDB-1p3y: MrsD from Bacillus sp. HIL-Y85/54728 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1p3y
TitleMrsD from Bacillus sp. HIL-Y85/54728
ComponentsMrsD protein
KeywordsOXIDOREDUCTASE / flavoprotein / FMN / Rossmann fold / HFCD family / oxdidative decarboxylation / cystein / lantibiotics / mersacidin
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / coenzyme A biosynthetic process / antibiotic biosynthetic process / FMN binding / oxidoreductase activity
Similarity search - Function
Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Mersacidin decarboxylase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsBlaesse, M. / Kupke, T. / Huber, R. / Steinbacher, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of MrsD, an FAD-binding protein of the HFCD family.
Authors: Blaesse, M. / Kupke, T. / Huber, R. / Steinbacher, S.
History
DepositionApr 19, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: MrsD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4942
Polymers21,7081
Non-polymers7861
Water1,15364
1
1: MrsD protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)269,92624
Polymers260,49912
Non-polymers9,42712
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation51_555-x+1/2,y,-z+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation74_555-x+1/2,-y+1/2,z1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
Buried area45080 Å2
ΔGint-268 kcal/mol
Surface area70500 Å2
MethodPISA, PQS
2
1: MrsD protein
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)539,85148
Polymers520,99824
Non-polymers18,85324
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_545y,z-1/2,x+1/21
crystal symmetry operation34_545-y,z-1/2,-x+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation36_555-y,-z+1/2,x+1/21
crystal symmetry operation41_545x,z-1/2,-y+1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation44_555x,-z+1/2,y+1/21
crystal symmetry operation53_455z-1/2,x,y+1/21
crystal symmetry operation54_455z-1/2,-x,-y+1/21
crystal symmetry operation55_555-z+1/2,-x,y+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation69_455z-1/2,y,-x+1/21
crystal symmetry operation70_455z-1/2,-y,x+1/21
crystal symmetry operation71_555-z+1/2,y,x+1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
Buried area81330 Å2
ΔGint-556 kcal/mol
Surface area149850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.769, 191.769, 191.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein MrsD protein


Mass: 21708.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: HIL-Y85/54728 / Gene: mrsD / Plasmid: pQE12 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9RC23
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.59 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: KNa tartrate, pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM1dropNaCl
220 mMTris-HCl1droppH8.0
310 mg/mlprotein1drop
41.2 Mpotassium/sodium tartrate tetrahydrate1reservoir
50.1 MTris-HCl1reservoirpH9.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.54→20 Å / Num. all: 10384 / Num. obs: 10384 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.2
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 5.4 / % possible all: 99.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MAINmodel building
CNS1.1refinement
MAINphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G5Q

1g5q


Resolution: 2.54→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 529 -random
Rwork0.2213 ---
obs0.222 10344 99.4 %-
all-10344 --
Refinement stepCycle: LAST / Resolution: 2.54→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 53 64 1461
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0105
X-RAY DIFFRACTIONc_angle_deg1.19
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS

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