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- PDB-1sbz: Crystal Structure of dodecameric FMN-dependent Ubix-like Decarbox... -

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Basic information

Entry
Database: PDB / ID: 1sbz
TitleCrystal Structure of dodecameric FMN-dependent Ubix-like Decarboxylase from Escherichia coli O157:H7
ComponentsProbable aromatic acid decarboxylase
KeywordsLYASE / FMN binding / Pad1 / UbiX / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / : / response to toxic substance
Similarity search - Function
Probable UbiX-like flavin prenyltransferase / Flavin prenyltransferase UbiX-like / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Probable UbiX-like flavin prenyltransferase / Probable UbiX-like flavin prenyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsRangarajan, E.S. / Li, Y. / Iannuzzi, P. / Tocilj, A. / Hung, L.-W. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Protein Sci. / Year: 2004
Title: Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7.
Authors: Rangarajan, E.S. / Li, Y. / Iannuzzi, P. / Tocilj, A. / Hung, L.-W. / Matte, A. / Cygler, M.
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable aromatic acid decarboxylase
B: Probable aromatic acid decarboxylase
C: Probable aromatic acid decarboxylase
D: Probable aromatic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8688
Polymers88,0434
Non-polymers1,8254
Water8,251458
1
A: Probable aromatic acid decarboxylase
B: Probable aromatic acid decarboxylase
C: Probable aromatic acid decarboxylase
D: Probable aromatic acid decarboxylase
hetero molecules

A: Probable aromatic acid decarboxylase
B: Probable aromatic acid decarboxylase
C: Probable aromatic acid decarboxylase
D: Probable aromatic acid decarboxylase
hetero molecules

A: Probable aromatic acid decarboxylase
B: Probable aromatic acid decarboxylase
C: Probable aromatic acid decarboxylase
D: Probable aromatic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,60524
Polymers264,12912
Non-polymers5,47612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area56090 Å2
ΔGint-381 kcal/mol
Surface area60970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.372, 95.372, 217.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological unit is a dodecamer and is assembled by by the operations : -Y, X-Y, Z & Y-X, -X, Z along with translation.

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Components

#1: Protein
Probable aromatic acid decarboxylase


Mass: 22010.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: PAD1, Z4047, ECS3593 / Plasmid: pFO4 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 (DE3)
References: UniProt: P69774, UniProt: P69772*PLUS, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 4K, 0.2M Lithium sulphate, 0.1M Hepes (7.0), VAPOR DIFFUSION, HANGING DROP, temperature 22K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9786, 0.9792, 0.9643
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2003 / Details: Mirrors
RadiationMonochromator: SILICONE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97921
30.96431
ReflectionResolution: 2→20 Å / Num. all: 56350 / Num. obs: 46319 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.066 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.15 Å / Rsym value: 0.377 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→19.32 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.315 / SU ML: 0.119 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21557 4137 8.9 %RANDOM
Rwork0.17648 ---
obs0.18012 42181 100 %-
all-46319 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.862 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5426 0 124 458 6008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225666
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9857721
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.70815932
X-RAY DIFFRACTIONr_chiral_restr0.0690.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024139
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22822
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2456
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7931.53704
X-RAY DIFFRACTIONr_mcangle_it0.94225784
X-RAY DIFFRACTIONr_scbond_it1.40732352
X-RAY DIFFRACTIONr_scangle_it2.0924.51937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 144 -
Rwork0.266 2268 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FMN.PARFMN.TOP

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