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- PDB-7p9q: Crystal structure of Indole 3-Carboxylic acid decarboxylase from ... -

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Basic information

Entry
Database: PDB / ID: 7p9q
TitleCrystal structure of Indole 3-Carboxylic acid decarboxylase from Arthrobacter nicotianae FI1612 in complex with co-factor prFMN.
ComponentsAnInD
KeywordsLYASE / AnInD
Function / homologyChem-4LU / :
Function and homology information
Biological speciesGlutamicibacter nicotianae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.53 Å
AuthorsGahloth, D. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC) United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural and biochemical characterization of the prenylated flavin mononucleotide-dependent indole-3-carboxylic acid decarboxylase.
Authors: Gahloth, D. / Fisher, K. / Payne, K.A.P. / Cliff, M. / Levy, C. / Leys, D.
History
DepositionJul 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
A: AnInD
B: AnInD
C: AnInD
D: AnInD
E: AnInD
F: AnInD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,22924
Polymers302,6096
Non-polymers3,62018
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29890 Å2
ΔGint-228 kcal/mol
Surface area92170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.200, 195.450, 105.210
Angle α, β, γ (deg.)90.000, 116.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 1 - 454 / Label seq-ID: 1 - 454

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
AnInD


Mass: 50434.785 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glutamicibacter nicotianae (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-4LU / 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol / prenylated-FMN iminium form


Mass: 525.469 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H30N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 Carboxylic acid, 0.1 M Buffer System pH 6.5, 30% Precipitant mixture 3

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.53→43.42 Å / Num. obs: 123931 / % possible obs: 98.86 % / Redundancy: 3.4 % / CC1/2: 0.994 / Net I/σ(I): 8.6
Reflection shellResolution: 2.53→2.57 Å / Num. unique obs: 6258 / CC1/2: 0.39

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ABO

7abo


Resolution: 2.53→43.42 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 26.958 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.393 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.221 6529 5.3 %RANDOM
Rwork0.1839 ---
obs0.1858 117399 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 280.65 Å2 / Biso mean: 84.096 Å2 / Biso min: 43.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-1.32 Å2
2--3.27 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 2.53→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20763 0 228 477 21468
Biso mean--109.26 79.55 -
Num. residues----2714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01321484
X-RAY DIFFRACTIONr_bond_other_d0.0020.01719699
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.63529302
X-RAY DIFFRACTIONr_angle_other_deg1.3651.57345574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2352703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02622.3121116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.063153276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7915132
X-RAY DIFFRACTIONr_chiral_restr0.0740.22767
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0224448
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024460
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A142130.02
12B142130.02
21A141330.03
22C141330.03
31A141270.03
32D141270.03
41A141100.03
42E141100.03
51A141170.03
52F141170.03
61B141670.02
62C141670.02
71B141820.02
72D141820.02
81B141580.02
82E141580.02
91B141650.02
92F141650.02
101C142650.01
102D142650.01
111C142050.02
112E142050.02
121C141990.02
122F141990.02
131D141950.02
132E141950.02
141D142040.02
142F142040.02
151E142260.01
152F142260.01
LS refinement shellResolution: 2.53→2.596 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 526 -
Rwork0.414 8679 -
all-9205 -
obs--99.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.249-0.5278-0.12972.49060.72881.1243-0.0057-0.02090.02380.2980.2244-0.51530.32150.1004-0.21870.13940.075-0.10640.0621-0.09160.208353.81423.37914.209
21.40241.0591-0.12052.7662-0.30910.4871-0.38720.15060.2484-0.74260.29970.1965-0.00040.0810.08750.3456-0.1317-0.1060.07690.08390.149439.85876.406-7.584
32.2076-0.57080.03121.4859-0.25581.71-0.0042-0.3672-0.0320.6129-0.11140.4770.0465-0.10910.11550.3562-0.11840.31320.1355-0.03520.4334-10.69721.03953.284
41.9020.0259-0.38731.5328-0.31121.95690.03470.01510.16350.0226-0.12850.70190.0838-0.39770.09380.0824-0.00830.13080.1376-0.16260.6695-23.20478.58433.227
51.5352-0.15690.1381.0461-0.07791.12070.10490.6162-0.5055-0.6522-0.1250.30470.06790.03310.02010.42980.0918-0.270.2756-0.29350.5687-5.23215.095-3.892
61.4396-0.3094-0.22331.1757-0.4481.748-0.0079-0.27990.1960.7597-0.0673-0.6047-0.76830.50810.07520.9549-0.2547-0.27630.3199-0.1160.404430.88584.41553.416
70.4453-0.0103-0.06341.12490.050.240.0544-0.0217-0.04870.0891-0.06150.1861-0.09540.00370.00710.051-0.01010.01770.0072-0.02120.100914.53649.8623.601
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 310
2X-RAY DIFFRACTION2B17 - 310
3X-RAY DIFFRACTION3C17 - 310
4X-RAY DIFFRACTION4D17 - 310
5X-RAY DIFFRACTION5E17 - 310
6X-RAY DIFFRACTION6F17 - 310
7X-RAY DIFFRACTION7A311 - 454
8X-RAY DIFFRACTION7B311 - 454
9X-RAY DIFFRACTION7C311 - 454
10X-RAY DIFFRACTION7D311 - 454
11X-RAY DIFFRACTION7E311 - 454
12X-RAY DIFFRACTION7F311 - 454

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