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- PDB-5bnc: Structure of heme binding protein MSMEG_6519 from Mycobacterium s... -

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Basic information

Entry
Database: PDB / ID: 5bnc
TitleStructure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis
Componentsheme binding protein MSMEG_6519
KeywordsHeme Binding Protein / heme oxygenase / split beta-barrel
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase / PNP-oxidase-like / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Split barrel-like / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll ...Pyridoxamine 5'-phosphate oxidase / PNP-oxidase-like / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Split barrel-like / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Pyridoxamine 5'-phosphate oxidase family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAhmed, F.H. / Carr, P.D. / Jackson, C.J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria.
Authors: Ahmed, F.H. / Carr, P.D. / Lee, B.M. / Afriat-Jurnou, L. / Mohamed, A.E. / Hong, N.S. / Flanagan, J. / Taylor, M.C. / Greening, C. / Jackson, C.J.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heme binding protein MSMEG_6519
B: heme binding protein MSMEG_6519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,77010
Polymers52,5792
Non-polymers1,1918
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-31 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 62.100, 301.406
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 25 - 265 / Label seq-ID: 11 - 251

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsdimer according to gel filtration

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein heme binding protein MSMEG_6519 / Pyridoxamine 5'-phosphate oxidase family protein / Pyridoxamine 5'-phosphate oxidase-related / FMN- ...Pyridoxamine 5'-phosphate oxidase family protein / Pyridoxamine 5'-phosphate oxidase-related / FMN-binding protein


Mass: 26289.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6519, MSMEI_6345, LJ00_32225 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R6E4

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Non-polymers , 5 types, 258 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M Magnesium Acetate, 0.1M Hepes, 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→43.77 Å / Num. obs: 31095 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.046 / Net I/σ(I): 14.1 / Num. measured all: 163129 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 99.2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
2.25-2.323.20.6371.9906728160.5160.417
9-43.775.20.02844.426055040.9990.013

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ARZ

2arz


Resolution: 2.25→43.77 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.624 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1588 5.1 %RANDOM
Rwork0.1846 ---
obs0.1869 29399 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.6 Å2 / Biso mean: 33.206 Å2 / Biso min: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å2-0 Å2
2---0.34 Å20 Å2
3---1.09 Å2
Refinement stepCycle: final / Resolution: 2.25→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 68 250 3940
Biso mean--46.37 36 -
Num. residues----494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193815
X-RAY DIFFRACTIONr_bond_other_d0.0050.023580
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9715228
X-RAY DIFFRACTIONr_angle_other_deg1.13338206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.0422.405158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47315529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3781539
X-RAY DIFFRACTIONr_chiral_restr0.0980.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214392
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02851
X-RAY DIFFRACTIONr_mcbond_it2.4743.141993
X-RAY DIFFRACTIONr_mcbond_other2.4693.1391992
X-RAY DIFFRACTIONr_mcangle_it3.7364.6982493
Refine LS restraints NCS

Ens-ID: 1 / Number: 12398 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 114 -
Rwork0.282 2148 -
all-2262 -
obs--98.78 %

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