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- PDB-8huc: Crystal structure of PaIch (Pec1) -

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Basic information

Entry
Database: PDB / ID: 8huc
TitleCrystal structure of PaIch (Pec1)
ComponentsMaoC_dehydrat_N domain-containing protein
KeywordsUNKNOWN FUNCTION / Hydro-lyase.
Function / homology: / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / HotDog domain superfamily / NITRATE ION / FAS1-like dehydratase domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.984 Å
AuthorsPramanik, A. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: Febs Lett. / Year: 2024
Title: Structural and functional insights of itaconyl-CoA hydratase from Pseudomonas aeruginosa highlight a novel N-terminal hotdog fold.
Authors: Pramanik, A. / Datta, S.
History
DepositionDec 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MaoC_dehydrat_N domain-containing protein
B: MaoC_dehydrat_N domain-containing protein
C: MaoC_dehydrat_N domain-containing protein
D: MaoC_dehydrat_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,82625
Polymers122,3144
Non-polymers1,51321
Water17,691982
1
A: MaoC_dehydrat_N domain-containing protein
C: MaoC_dehydrat_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,02114
Polymers61,1572
Non-polymers86412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-5 kcal/mol
Surface area22610 Å2
MethodPISA
2
B: MaoC_dehydrat_N domain-containing protein
D: MaoC_dehydrat_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,80511
Polymers61,1572
Non-polymers6489
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-6 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.312, 66.197, 77.462
Angle α, β, γ (deg.)102.45, 95.07, 101.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
MaoC_dehydrat_N domain-containing protein


Mass: 30578.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: PA14_52910 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0H2Z790
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 200mM Potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.9→31.76 Å / Num. obs: 83791 / % possible obs: 98.2 % / Redundancy: 18.86 % / Rrim(I) all: 0.13 / Net I/σ(I): 19.2
Reflection shellResolution: 1.98→2.05 Å / Num. unique obs: 7025 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PROTEUMv3.0data reduction
PROTEUMv3.0data scaling
AutoSolphasing
Cootmodel building
PHENIXv1.14refinement
RefinementMethod to determine structure: MIR / Resolution: 1.984→27.586 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 24.29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2206 1843 2.39 %
Rwork0.1822 --
obs0.1831 77191 90.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.984→27.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8197 0 98 982 9277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128559
X-RAY DIFFRACTIONf_angle_d1.16811612
X-RAY DIFFRACTIONf_dihedral_angle_d3.8716384
X-RAY DIFFRACTIONf_chiral_restr0.0581178
X-RAY DIFFRACTIONf_plane_restr0.0091568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.984-2.03720.3332950.30784234X-RAY DIFFRACTION66
2.0372-2.09710.28181490.26485548X-RAY DIFFRACTION87
2.0971-2.16480.3231240.24055548X-RAY DIFFRACTION87
2.1648-2.24210.30411400.21755560X-RAY DIFFRACTION87
2.2421-2.33180.27231420.20155656X-RAY DIFFRACTION88
2.3318-2.43790.24571390.18835760X-RAY DIFFRACTION90
2.4379-2.56640.2391420.18915867X-RAY DIFFRACTION92
2.5664-2.7270.24261380.18626016X-RAY DIFFRACTION94
2.727-2.93730.22441640.18055967X-RAY DIFFRACTION94
2.9373-3.23250.2311480.17936209X-RAY DIFFRACTION96
3.2325-3.69930.1731540.15446257X-RAY DIFFRACTION98
3.6993-4.65710.16431570.13536370X-RAY DIFFRACTION99
4.6571-27.5860.1811510.16666356X-RAY DIFFRACTION99

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