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- PDB-6vna: Pden_1323 -

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Basic information

Entry
Database: PDB / ID: 6vna
TitlePden_1323
ComponentsPyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
KeywordsMETAL BINDING PROTEIN / Heme
Function / homologyHeme utilization protein HutZ / CREG, beta-barrel / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
Function and homology information
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIsiorho, E.A. / Mansoorabadi, S.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A noncanonical heme oxygenase specific for the degradation of c-type heme.
Authors: Li, S. / Isiorho, E.A. / Owens, V.L. / Donnan, P.H. / Odili, C.L. / Mansoorabadi, S.O.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
C: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Theoretical massNumber of molelcules
Total (without water)52,1073
Polymers52,1073
Non-polymers00
Water84747
1
A: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
C: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Theoretical massNumber of molelcules
Total (without water)34,7382
Polymers34,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-21 kcal/mol
Surface area13190 Å2
MethodPISA
2
B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein

B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Theoretical massNumber of molelcules
Total (without water)34,7382
Polymers34,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2750 Å2
ΔGint-23 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.843, 117.044, 59.382
Angle α, β, γ (deg.)90.000, 99.376, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein


Mass: 17368.971 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_1323, Pden_1574 / Production host: Escherichia coli (E. coli) / References: UniProt: A1B1N4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: glycerol, PEG 4000, sodium acetate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2018
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→61.25 Å / Num. obs: 32977 / % possible obs: 99.7 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 1677 / CC1/2: 0.582

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: itasser

Resolution: 2.2→58.657 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.214
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2587 1294 5.215 %
Rwork0.2115 --
all0.214 --
obs-24814 99.595 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.131 Å2
Baniso -1Baniso -2Baniso -3
1--2.995 Å20 Å2-3.54 Å2
2---3.766 Å20 Å2
3---7.519 Å2
Refinement stepCycle: LAST / Resolution: 2.2→58.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 0 47 3197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133210
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173187
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6434360
X-RAY DIFFRACTIONr_angle_other_deg2.3461.5787305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9985414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.86919.07172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75915518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5461540
X-RAY DIFFRACTIONr_chiral_restr0.0590.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023615
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02701
X-RAY DIFFRACTIONr_nbd_refined0.2030.2509
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.22683
X-RAY DIFFRACTIONr_nbtor_refined0.1430.21431
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0720.29
X-RAY DIFFRACTIONr_nbd_other0.2190.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.23
X-RAY DIFFRACTIONr_mcbond_it5.0536.4691671
X-RAY DIFFRACTIONr_mcbond_other5.0466.4681670
X-RAY DIFFRACTIONr_mcangle_it7.3889.682077
X-RAY DIFFRACTIONr_mcangle_other7.3899.6822078
X-RAY DIFFRACTIONr_scbond_it5.327.2661538
X-RAY DIFFRACTIONr_scbond_other5.3197.2691539
X-RAY DIFFRACTIONr_scangle_it8.34710.6452282
X-RAY DIFFRACTIONr_scangle_other8.34610.6472283
X-RAY DIFFRACTIONr_lrange_it11.32375.8613140
X-RAY DIFFRACTIONr_lrange_other11.32775.8623135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.4151080.3761677X-RAY DIFFRACTION98.892
2.257-2.3190.324850.3731695X-RAY DIFFRACTION99.4969
2.319-2.3860.403980.3461637X-RAY DIFFRACTION99.1995
2.386-2.4590.369820.3241607X-RAY DIFFRACTION99.5286
2.459-2.540.284940.2991539X-RAY DIFFRACTION99.4519
2.54-2.6290.321700.2771500X-RAY DIFFRACTION99.6193
2.629-2.7280.315730.2421450X-RAY DIFFRACTION99.5425
2.728-2.8390.303650.2291390X-RAY DIFFRACTION99.7942
2.839-2.9650.3660.2161362X-RAY DIFFRACTION99.7904
2.965-3.1090.249750.1931267X-RAY DIFFRACTION99.7028
3.109-3.2770.309760.1981223X-RAY DIFFRACTION99.7696
3.277-3.4750.208660.1771145X-RAY DIFFRACTION99.8351
3.475-3.7140.235710.1891060X-RAY DIFFRACTION99.9117
3.714-4.010.262550.1911014X-RAY DIFFRACTION99.9065
4.01-4.3910.183450.157938X-RAY DIFFRACTION99.8984
4.391-4.9070.195390.163858X-RAY DIFFRACTION99.8886
4.907-5.660.265480.189733X-RAY DIFFRACTION99.8721
5.66-6.9170.227340.224642X-RAY DIFFRACTION100
6.917-9.720.272230.208502X-RAY DIFFRACTION100
9.72-58.6570.234210.226281X-RAY DIFFRACTION99.67

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