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- PDB-7cfu: Crystal Structure of FMN-dependent Cysteine Decarboxylases SpaF -

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Basic information

Entry
Database: PDB / ID: 7cfu
TitleCrystal Structure of FMN-dependent Cysteine Decarboxylases SpaF
ComponentsDNA/pantothenate metabolism flavoprotein
KeywordsBIOSYNTHETIC PROTEIN / FMN-dependent
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / coenzyme A biosynthetic process / FMN binding
Similarity search - Function
Flavoprotein / Flavin prenyltransferase-like / Flavoprotein
Similarity search - Domain/homology
ARGININE / FLAVIN MONONUCLEOTIDE / DNA/pantothenate metabolism flavoprotein
Similarity search - Component
Biological speciesStreptomyces sparsogenes DSM 40356 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLi, J. / Lu, J. / Wang, H. / Zhu, J.
CitationJournal: To Be Published
Title: Characterization of FMN-dependent Cysteine Decarboxylases SPAF
Authors: Lu, J. / Li, J. / Zhu, J. / Wang, H.
History
DepositionJun 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: DNA/pantothenate metabolism flavoprotein
S: DNA/pantothenate metabolism flavoprotein
H: DNA/pantothenate metabolism flavoprotein
P: DNA/pantothenate metabolism flavoprotein
A: DNA/pantothenate metabolism flavoprotein
B: DNA/pantothenate metabolism flavoprotein
C: DNA/pantothenate metabolism flavoprotein
D: DNA/pantothenate metabolism flavoprotein
E: DNA/pantothenate metabolism flavoprotein
G: DNA/pantothenate metabolism flavoprotein
I: DNA/pantothenate metabolism flavoprotein
J: DNA/pantothenate metabolism flavoprotein
K: DNA/pantothenate metabolism flavoprotein
L: DNA/pantothenate metabolism flavoprotein
M: DNA/pantothenate metabolism flavoprotein
N: DNA/pantothenate metabolism flavoprotein
O: DNA/pantothenate metabolism flavoprotein
Q: DNA/pantothenate metabolism flavoprotein
R: DNA/pantothenate metabolism flavoprotein
T: DNA/pantothenate metabolism flavoprotein
U: DNA/pantothenate metabolism flavoprotein
V: DNA/pantothenate metabolism flavoprotein
W: DNA/pantothenate metabolism flavoprotein
X: DNA/pantothenate metabolism flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)539,29949
Polymers528,17124
Non-polymers11,12725
Water31,0401723
1
F: DNA/pantothenate metabolism flavoprotein
S: DNA/pantothenate metabolism flavoprotein
H: DNA/pantothenate metabolism flavoprotein
P: DNA/pantothenate metabolism flavoprotein
D: DNA/pantothenate metabolism flavoprotein
E: DNA/pantothenate metabolism flavoprotein
G: DNA/pantothenate metabolism flavoprotein
L: DNA/pantothenate metabolism flavoprotein
M: DNA/pantothenate metabolism flavoprotein
N: DNA/pantothenate metabolism flavoprotein
T: DNA/pantothenate metabolism flavoprotein
U: DNA/pantothenate metabolism flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,73725
Polymers264,08612
Non-polymers5,65113
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41140 Å2
ΔGint-236 kcal/mol
Surface area67870 Å2
MethodPISA
2
A: DNA/pantothenate metabolism flavoprotein
B: DNA/pantothenate metabolism flavoprotein
C: DNA/pantothenate metabolism flavoprotein
I: DNA/pantothenate metabolism flavoprotein
J: DNA/pantothenate metabolism flavoprotein
K: DNA/pantothenate metabolism flavoprotein
V: DNA/pantothenate metabolism flavoprotein
W: DNA/pantothenate metabolism flavoprotein
X: DNA/pantothenate metabolism flavoprotein
hetero molecules

O: DNA/pantothenate metabolism flavoprotein
Q: DNA/pantothenate metabolism flavoprotein
R: DNA/pantothenate metabolism flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,56224
Polymers264,08612
Non-polymers5,47612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area41040 Å2
ΔGint-236 kcal/mol
Surface area67810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.629, 189.609, 185.349
Angle α, β, γ (deg.)90.000, 92.520, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAILEILE(chain 'A' and (resid 18 through 34 or (resid 35...AE18 - 17218 - 172
12PROPROALAALA(chain 'A' and (resid 18 through 34 or (resid 35...AE181 - 199181 - 199
13FMNFMNFMNFMN(chain 'A' and (resid 18 through 34 or (resid 35...ADA301
21ALAALAILEILE(chain 'B' and (resid 18 through 34 or (resid 35...BF18 - 17218 - 172
22PROPROALAALA(chain 'B' and (resid 18 through 34 or (resid 35...BF181 - 199181 - 199
23FMNFMNFMNFMN(chain 'B' and (resid 18 through 34 or (resid 35...BEA301
31ALAALAILEILE(chain 'C' and (resid 18 through 34 or (resid 35...CG18 - 17218 - 172
32PROPROALAALA(chain 'C' and (resid 18 through 34 or (resid 35...CG181 - 199181 - 199
33FMNFMNFMNFMN(chain 'C' and (resid 18 through 34 or (resid 35...CFA301
41ALAALAILEILE(chain 'D' and (resid 18 through 34 or (resid 35...DH18 - 17218 - 172
42PROPROALAALA(chain 'D' and (resid 18 through 34 or (resid 35...DH181 - 199181 - 199
43FMNFMNFMNFMN(chain 'D' and (resid 18 through 34 or (resid 35...DGA301
51ALAALAILEILE(chain 'E' and (resid 18 through 34 or (resid 35...EI18 - 17218 - 172
52PROPROALAALA(chain 'E' and (resid 18 through 34 or (resid 35...EI181 - 199181 - 199
53FMNFMNFMNFMN(chain 'E' and (resid 18 through 34 or (resid 35...EHA301
61ALAALAILEILE(chain 'F' and (resid 18 through 34 or (resid 35...FA18 - 17218 - 172
62PROPROALAALA(chain 'F' and (resid 18 through 34 or (resid 35...FA181 - 199181 - 199
63FMNFMNFMNFMN(chain 'F' and (resid 18 through 34 or (resid 35...FY301
71ALAALAILEILE(chain 'G' and (resid 18 through 34 or (resid 35...GJ18 - 17218 - 172
72PROPROALAALA(chain 'G' and (resid 18 through 34 or (resid 35...GJ181 - 199181 - 199
73FMNFMNFMNFMN(chain 'G' and (resid 18 through 34 or (resid 35...GIA301
81ALAALAILEILE(chain 'H' and (resid 18 through 34 or (resid 35...HC18 - 17218 - 172
82PROPROALAALA(chain 'H' and (resid 18 through 34 or (resid 35...HC181 - 199181 - 199
83FMNFMNFMNFMN(chain 'H' and (resid 18 through 34 or (resid 35...HBA301
91ALAALAILEILE(chain 'I' and (resid 18 through 34 or (resid 35...IK18 - 17218 - 172
92PROPROALAALA(chain 'I' and (resid 18 through 34 or (resid 35...IK181 - 199181 - 199
93FMNFMNFMNFMN(chain 'I' and (resid 18 through 34 or (resid 35...IJA301
101ALAALAILEILE(chain 'J' and (resid 18 through 34 or (resid 35...JL18 - 17218 - 172
102PROPROALAALA(chain 'J' and (resid 18 through 34 or (resid 35...JL181 - 199181 - 199
103FMNFMNFMNFMN(chain 'J' and (resid 18 through 34 or (resid 35...JKA301
111ALAALAILEILE(chain 'K' and (resid 18 through 34 or (resid 35...KM18 - 17218 - 172
112PROPROALAALA(chain 'K' and (resid 18 through 34 or (resid 35...KM181 - 199181 - 199
113FMNFMNFMNFMN(chain 'K' and (resid 18 through 34 or (resid 35...KLA301
121ALAALAILEILE(chain 'L' and (resid 18 through 34 or (resid 35...LN18 - 17218 - 172
122PROPROALAALA(chain 'L' and (resid 18 through 34 or (resid 35...LN181 - 199181 - 199
123FMNFMNFMNFMN(chain 'L' and (resid 18 through 34 or (resid 35...LMA301
131ALAALAILEILE(chain 'M' and (resid 18 through 34 or (resid 35...MO18 - 17218 - 172
132PROPROALAALA(chain 'M' and (resid 18 through 34 or (resid 35...MO181 - 199181 - 199
133FMNFMNFMNFMN(chain 'M' and (resid 18 through 34 or (resid 35...MNA301
141ALAALAILEILE(chain 'N' and (resid 18 through 34 or (resid 35...NP18 - 17218 - 172
142PROPROALAALA(chain 'N' and (resid 18 through 34 or (resid 35...NP181 - 199181 - 199
143FMNFMNFMNFMN(chain 'N' and (resid 18 through 34 or (resid 35...NOA301
151ALAALAILEILE(chain 'O' and (resid 18 through 34 or (resid 35...OQ18 - 17218 - 172
152PROPROALAALA(chain 'O' and (resid 18 through 34 or (resid 35...OQ181 - 199181 - 199
153FMNFMNFMNFMN(chain 'O' and (resid 18 through 34 or (resid 35...OPA301
161ALAALAILEILE(chain 'P' and (resid 18 through 34 or (resid 35...PD18 - 17218 - 172
162PROPROALAALA(chain 'P' and (resid 18 through 34 or (resid 35...PD181 - 199181 - 199
163FMNFMNFMNFMN(chain 'P' and (resid 18 through 34 or (resid 35...PCA301
171ALAALAILEILE(chain 'Q' and (resid 18 through 34 or (resid 35...QR18 - 17218 - 172
172PROPROALAALA(chain 'Q' and (resid 18 through 34 or (resid 35...QR181 - 199181 - 199
173FMNFMNFMNFMN(chain 'Q' and (resid 18 through 34 or (resid 35...QQA301
181ALAALAILEILE(chain 'R' and (resid 18 through 34 or (resid 35...RS18 - 17218 - 172
182PROPROALAALA(chain 'R' and (resid 18 through 34 or (resid 35...RS181 - 199181 - 199
183FMNFMNFMNFMN(chain 'R' and (resid 18 through 34 or (resid 35...RRA301
191ALAALAILEILE(chain 'S' and (resid 18 through 200 or resid 301))SB18 - 17218 - 172
192PROPROALAALA(chain 'S' and (resid 18 through 200 or resid 301))SB181 - 199181 - 199
193ARGARGARGARG(chain 'S' and (resid 18 through 200 or resid 301))SZ301
201ALAALAILEILE(chain 'T' and (resid 18 through 34 or (resid 35...TT18 - 17218 - 172
202PROPROALAALA(chain 'T' and (resid 18 through 34 or (resid 35...TT181 - 199181 - 199
203FMNFMNFMNFMN(chain 'T' and (resid 18 through 34 or (resid 35...TSA301
211ALAALAILEILE(chain 'U' and (resid 18 through 34 or (resid 35...UU18 - 17218 - 172
212PROPROALAALA(chain 'U' and (resid 18 through 34 or (resid 35...UU181 - 199181 - 199
213FMNFMNFMNFMN(chain 'U' and (resid 18 through 34 or (resid 35...UTA301
221ALAALAILEILE(chain 'V' and (resid 18 through 34 or (resid 35...VV18 - 17218 - 172
222PROPROALAALA(chain 'V' and (resid 18 through 34 or (resid 35...VV181 - 199181 - 199
223FMNFMNFMNFMN(chain 'V' and (resid 18 through 34 or (resid 35...VUA301
231ALAALAILEILE(chain 'W' and (resid 18 through 34 or (resid 35...WW18 - 17218 - 172
232PROPROALAALA(chain 'W' and (resid 18 through 34 or (resid 35...WW181 - 199181 - 199
233FMNFMNFMNFMN(chain 'W' and (resid 18 through 34 or (resid 35...WVA301
241ALAALAILEILE(chain 'X' and (resid 18 through 34 or (resid 35...XX18 - 17218 - 172
242PROPROALAALA(chain 'X' and (resid 18 through 34 or (resid 35...XX181 - 199181 - 199
243FMNFMNFMNFMN(chain 'X' and (resid 18 through 34 or (resid 35...XWA301

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Components

#1: Protein ...
DNA/pantothenate metabolism flavoprotein / FMN-dependent Cysteine Decarboxylases SpaF


Mass: 22007.137 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sparsogenes DSM 40356 (bacteria)
Gene: SPAR_40642 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1R1S5L5
#2: Chemical...
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1723 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.15 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 2.0M NaCl, 0.1M potassium phosphate mono basic, 0.1M sodium phosphate monobasic, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→48.96 Å / Num. obs: 345160 / % possible obs: 97.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.79 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.8
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 17051 / CC1/2: 0.589

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Processing

Software
NameVersionClassification
PHENIX1.14_3235refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JLS

6jls


Resolution: 2.15→48.96 Å / SU ML: 0.2698 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.8581 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 17287 5.02 %
Rwork0.203 327069 -
obs0.2046 344356 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.54 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30737 0 755 1723 33215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532163
X-RAY DIFFRACTIONf_angle_d0.706244061
X-RAY DIFFRACTIONf_chiral_restr0.05025185
X-RAY DIFFRACTIONf_plane_restr0.00475514
X-RAY DIFFRACTIONf_dihedral_angle_d10.61118655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.33755900.306310774X-RAY DIFFRACTION97.05
2.17-2.20.33596210.294611035X-RAY DIFFRACTION98.84
2.2-2.230.3085690.279810943X-RAY DIFFRACTION98.72
2.23-2.250.34246220.291511060X-RAY DIFFRACTION98.58
2.25-2.280.31675910.278710885X-RAY DIFFRACTION98.73
2.28-2.320.2816020.25511038X-RAY DIFFRACTION98.85
2.32-2.350.29665810.250911017X-RAY DIFFRACTION98.9
2.35-2.380.28486220.244910930X-RAY DIFFRACTION98.52
2.38-2.420.28295930.24110995X-RAY DIFFRACTION98.35
2.42-2.460.27685210.238811041X-RAY DIFFRACTION98.47
2.46-2.50.28565470.232710979X-RAY DIFFRACTION98.33
2.5-2.550.2665580.231211049X-RAY DIFFRACTION98.44
2.55-2.60.26025780.229110927X-RAY DIFFRACTION98.63
2.6-2.650.295810.238711030X-RAY DIFFRACTION98.22
2.65-2.710.26096110.226910948X-RAY DIFFRACTION98.08
2.71-2.770.25935830.215910714X-RAY DIFFRACTION96.8
2.77-2.840.25695650.211510791X-RAY DIFFRACTION96.55
2.84-2.920.23175260.207910842X-RAY DIFFRACTION96.67
2.92-30.26095130.215710500X-RAY DIFFRACTION93.71
3-3.10.26054880.21389790X-RAY DIFFRACTION87.57
3.1-3.210.24215280.208810877X-RAY DIFFRACTION96.69
3.21-3.340.24075970.209111044X-RAY DIFFRACTION99.06
3.34-3.490.2295930.196811117X-RAY DIFFRACTION99.24
3.49-3.680.21936590.191611047X-RAY DIFFRACTION99.46
3.68-3.910.21195660.184511150X-RAY DIFFRACTION99.59
3.91-4.210.20195850.174711159X-RAY DIFFRACTION99.51
4.21-4.630.18865440.16211160X-RAY DIFFRACTION99.04
4.63-5.30.18635290.167911118X-RAY DIFFRACTION98.21
5.3-6.680.21765770.196710057X-RAY DIFFRACTION90
6.68-48.960.2026470.168411052X-RAY DIFFRACTION97.66

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