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- PDB-2v7i: PrnB native -

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Basic information

Entry
Database: PDB / ID: 2v7i
TitlePrnB native
ComponentsPRNB
KeywordsBIOSYNTHETIC PROTEIN / HEME / IDO / TDO
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 / tryptophan catabolic process to 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
PROTOPORPHYRIN IX CONTAINING FE / Monodechloroaminopyrrolnitrin synthase PrnB
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNaismith, J.H.
CitationJournal: Biochemistry / Year: 2007
Title: The Second Enzyme in Pyrrolnitrin Biosynthetic Pathway is Related to the Heme-Dependent Dioxygenase Superfamily
Authors: De Laurentis, W. / Khim, L. / Anderson, J.L.R. / Adam, A. / Phillips, R.S. / Chapman, S.K. / Van Pee, K.-H. / Naismith, J.H.
History
DepositionJul 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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_conn
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRNB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7264
Polymers39,9171
Non-polymers8093
Water6,684371
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.798, 80.120, 129.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2143-

HOH

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Components

#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) / Production host: PSEUDOMONAS FLUORESCENS (bacteria) / References: UniProt: P95481
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
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
Sequence detailsTRIPLE MUTANT CRYSTALLIZED

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.75→38 Å / Num. obs: 33422 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 1.75→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V7J

2v7j


Resolution: 1.75→64.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.563 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1759 5 %RANDOM
Rwork0.179 ---
obs0.18 33422 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å20 Å2
2---0.96 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→64.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 53 371 3150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222877
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2062.0313939
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9835353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43122.171129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2115443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9381530
X-RAY DIFFRACTIONr_chiral_restr0.0790.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022269
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21489
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22025
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2300
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6381.51802
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01922823
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57231546
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7284.51112
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 136
Rwork0.227 2312
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)
10.55080.10980.01870.7597-0.43211.2394-0.00870.09560.0103-0.14160.00010.0198-0.0533-0.02820.0086-0.2090.01730.0146-0.1228-0.0084-0.0999-16.59810.45917.938
213.98-1.34660.859310.19041.37125.95310.4176-0.1756-0.4049-0.0267-0.3321-0.02380.55490.5733-0.0855-0.09880.00560.0207-0.08770.0102-0.1401-12.9934.33412.975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 361
2X-RAY DIFFRACTION2A1362

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