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- PDB-2x67: The ternary complex of PrnB (the second enzyme in pyrrolnitrin bi... -

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Basic information

Entry
Database: PDB / ID: 2x67
TitleThe ternary complex of PrnB (the second enzyme in pyrrolnitrin biosynthesis pathway), tryptophan and cyanide
ComponentsPRNB
KeywordsBIOSYNTHETIC PROTEIN / INDOLAMINE/TRYPTOPHAN DIOXYGENASE SUPERFAMILY
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of water / L-tryptophan catabolic process to L-kynurenine / antibiotic biosynthetic process / oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1320 / Monodechloroaminopyrrolnitrin synthase PrnB / Monodechloroaminopyrrolnitrin synthase PrnB / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #480 / Tryptophan/Indoleamine 2,3-dioxygenase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / TRYPTOPHAN / Monodechloroaminopyrrolnitrin synthase PrnB
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsZhu, X. / van pee, K.-H. / Naismith, J.H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The Ternary Complex of Prnb (the Second Enzyme in Pyrrolnitrin Biosynthesis Pathway), Tryptophan and Cyanide Yields New Mechanistic Insights Into the Indolamine Dioxygenase Superfamily.
Authors: Zhu, X. / Van Pee, K.-H. / Naismith, J.H.
History
DepositionFeb 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRNB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9566
Polymers39,9171
Non-polymers1,0395
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.392, 79.441, 92.058
Angle α, β, γ (deg.)90.00, 103.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PRNB


Mass: 39917.492 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: BL915 / Plasmid: PCIBHISTEVPRNB_TRIPLE_CYSMUTANT / Production host: PSEUDOMONAS FLUORESCENS (bacteria) / Strain (production host): BL915 / Variant (production host): DELTAORF(PRNA-PRND) / References: UniProt: P95481

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Non-polymers , 5 types, 309 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 21 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 60 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 21 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 60 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 175 TO SER

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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: 2.9 Å3/Da / Density % sol: 57.97 % / Description: NONE
Crystal growpH: 6.4
Details: 0.1M BIS-TRIS BUFFER PH 6.4, 10% PEG3350, 0.2M MGSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Apr 17, 2008 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.16→30 Å / Num. obs: 24411 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V7J

2v7j


Resolution: 2.16→29.84 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.596 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21073 1330 5.2 %RANDOM
Rwork0.16556 ---
obs0.16788 24411 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.024 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.56 Å2
2---0.73 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.16→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 70 304 3111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222917
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3712.0283990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0575356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.54822.061131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65715450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.611531
X-RAY DIFFRACTIONr_chiral_restr0.0920.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6381.51777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16722852
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12231140
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4664.51138
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 95 -
Rwork0.194 1755 -
obs--98.77 %
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)
11.0282-0.01230.11552.55020.38230.69750.0320.1438-0.0325-0.1724-0.07-0.0274-0.01620.00680.0380.02360.00810.00180.1060.0140.096315.849716.3031-3.2058
20.4628-0.2702-0.09771.46450.58211.3002-0.0256-0.1061-0.00810.23160.029-0.0367-0.01480.0462-0.00350.0479-0.0052-0.0090.07040.02410.085117.288923.38114.4336
30.79990.97790.87914.07292.34833.3605-0.0361-0.129-0.10570.6182-0.05750.00760.2005-0.05580.09360.2255-0.00260.00860.14680.05240.063516.539527.245531.6628
42.5477-3.7763-3.83210.98750.66077.1673-0.0803-0.1107-0.06810.23050.12860.30480.1130.1753-0.04830.05260.01990.0090.01970.00120.008513.503716.633919.5628
511.5561-18.151722.930263.9341-27.931345.260.1854-0.54310.1414-0.4682-0.27970.10810.915-1.1920.09420.31030.0059-0.06580.19570.01310.218712.944813.810114.5404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 93
2X-RAY DIFFRACTION2A94 - 270
3X-RAY DIFFRACTION3A271 - 358
4X-RAY DIFFRACTION4A1359
5X-RAY DIFFRACTION4A1363
6X-RAY DIFFRACTION5A1360

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