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- PDB-5kvs: Substrate Analog and NADP+ bound structure of Irp3, a Thiazolinyl... -

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Basic information

Entry
Database: PDB / ID: 5kvs
TitleSubstrate Analog and NADP+ bound structure of Irp3, a Thiazolinyl Imine Reductase from Yersinia enterocolitica
ComponentsIrp3 protein
KeywordsOXIDOREDUCTASE / imine reductase / Irp3 / siderophore / substrate analog / HPTT-COOH / yersiniabactin
Function / homology
Function and homology information


Thiazolinyl imide reductase / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6XR / FORMIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Irp3 protein
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsMeneely, K.M. / Lamb, A.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI77725 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K02 AI093675 United States
National Science Foundation (NSF, United States)CHE-1403293 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM08545 United States
CitationJournal: Biochemistry / Year: 2016
Title: Holo Structure and Steady State Kinetics of the Thiazolinyl Imine Reductases for Siderophore Biosynthesis.
Authors: Meneely, K.M. / Ronnebaum, T.A. / Riley, A.P. / Prisinzano, T.E. / Lamb, A.L.
History
DepositionJul 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Irp3 protein
B: Irp3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,16910
Polymers85,8542
Non-polymers2,3168
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-62 kcal/mol
Surface area26070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.389, 148.553, 65.396
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Irp3 protein


Mass: 42926.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: irp3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O54512

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Non-polymers , 5 types, 482 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-6XR / (4~{R})-2-[2-(2-hydroxyphenyl)-1,3-thiazol-4-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid


Mass: 306.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10N2O3S2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.2 M sodium formate, pH 7.3, 20% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1887 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2013 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1887 Å / Relative weight: 1
ReflectionResolution: 1.28→39.42 Å / Num. obs: 196862 / % possible obs: 96.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.26 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.5
Reflection shellResolution: 1.28→1.34 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.5 / % possible all: 84.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KVQ

5kvq


Resolution: 1.28→36.037 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.06
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 9896 5.03 %Random selection
Rwork0.1616 ---
obs0.1622 196796 96.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 1.28→36.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5563 0 150 474 6187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086115
X-RAY DIFFRACTIONf_angle_d1.2528410
X-RAY DIFFRACTIONf_dihedral_angle_d16.1452248
X-RAY DIFFRACTIONf_chiral_restr0.081923
X-RAY DIFFRACTIONf_plane_restr0.0081077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2751-1.28960.29641900.28573750X-RAY DIFFRACTION58
1.2896-1.30480.26422970.25335248X-RAY DIFFRACTION82
1.3048-1.32070.25833120.24245983X-RAY DIFFRACTION93
1.3207-1.33740.23613150.22066457X-RAY DIFFRACTION100
1.3374-1.3550.21283200.22656358X-RAY DIFFRACTION100
1.355-1.37360.25073420.21546474X-RAY DIFFRACTION100
1.3736-1.39320.20653870.21596355X-RAY DIFFRACTION100
1.3932-1.4140.23313660.20856381X-RAY DIFFRACTION100
1.414-1.43610.22142910.19926483X-RAY DIFFRACTION100
1.4361-1.45960.20733170.19216382X-RAY DIFFRACTION100
1.4596-1.48480.19563550.18266451X-RAY DIFFRACTION100
1.4848-1.51180.20773420.17456355X-RAY DIFFRACTION100
1.5118-1.54090.19283550.16936382X-RAY DIFFRACTION99
1.5409-1.57230.18963140.16466425X-RAY DIFFRACTION99
1.5723-1.60650.18863420.1616360X-RAY DIFFRACTION99
1.6065-1.64390.18893560.166368X-RAY DIFFRACTION99
1.6439-1.6850.16633310.15136327X-RAY DIFFRACTION98
1.685-1.73060.16843550.14926328X-RAY DIFFRACTION98
1.7306-1.78150.17693140.15266312X-RAY DIFFRACTION98
1.7815-1.8390.18473340.15226301X-RAY DIFFRACTION98
1.839-1.90470.15973250.15216348X-RAY DIFFRACTION98
1.9047-1.9810.17113580.15076296X-RAY DIFFRACTION98
1.981-2.07110.15223270.14856311X-RAY DIFFRACTION98
2.0711-2.18030.16033380.1496314X-RAY DIFFRACTION98
2.1803-2.31690.16343230.14636264X-RAY DIFFRACTION98
2.3169-2.49570.15673080.14096316X-RAY DIFFRACTION98
2.4957-2.74680.15623270.156361X-RAY DIFFRACTION98
2.7468-3.14410.17983590.15826341X-RAY DIFFRACTION99
3.1441-3.96040.15733610.15676361X-RAY DIFFRACTION99
3.9604-36.05110.16873350.16436508X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.9785 Å / Origin y: 36.1634 Å / Origin z: 15.62 Å
111213212223313233
T0.0659 Å20.0064 Å2-0.0003 Å2-0.1141 Å2-0.0001 Å2--0.0887 Å2
L0.2021 °2-0.0144 °2-0.0494 °2-0.9038 °2-0.2077 °2--0.3335 °2
S0.0175 Å °0.0091 Å °0.0074 Å °-0.0231 Å °0.0226 Å °0.0694 Å °-0.0265 Å °-0.0196 Å °-0.038 Å °
Refinement TLS groupSelection details: all

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