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- PDB-4ybn: Structure of the FAD and Heme binding protein msmeg_4975 from Myc... -

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Basic information

Entry
Database: PDB / ID: 4ybn
TitleStructure of the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis
ComponentsFlavin-nucleotide-binding protein
KeywordsOXIDOREDUCTASE / FAD / Heme / split beta-barrel
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Pyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / Flavin-nucleotide-binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAhmed, F.H. / Carr, P.D. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
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
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references / Derived calculations
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _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
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.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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-nucleotide-binding protein
B: Flavin-nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,74611
Polymers47,5732
Non-polymers3,1739
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-153 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.722, 59.876, 89.658
Angle α, β, γ (deg.)90.000, 93.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Flavin-nucleotide-binding protein / Pyridoxamine 5'-phosphate oxidase-related / FMN-binding protein


Mass: 23786.686 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_4975, MSMEI_4848, LJ00_24605 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R238

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Non-polymers , 6 types, 333 molecules

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


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 20% PEG1500, 4% MPD, 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9655 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.9→44.73 Å / Num. obs: 35306 / % possible obs: 99.6 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13 / Num. measured all: 264436 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2% possible all
1.9-1.947.61.1092.11710322570.7699.2
9.11-44.736.70.0440.823323470.99698.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 2FUR

2fur


Resolution: 1.9→44.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.124 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 1749 5 %RANDOM
Rwork0.1738 ---
obs0.1763 33553 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.73 Å2 / Biso mean: 33.33 Å2 / Biso min: 15.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å2-0 Å2-0.15 Å2
2--2.21 Å20 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.9→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 208 326 3654
Biso mean--39.37 41.59 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193582
X-RAY DIFFRACTIONr_bond_other_d0.0020.023276
X-RAY DIFFRACTIONr_angle_refined_deg1.8962.0454966
X-RAY DIFFRACTIONr_angle_other_deg0.89437525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83322.59139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65215501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2541534
X-RAY DIFFRACTIONr_chiral_restr0.1270.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214113
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02805
X-RAY DIFFRACTIONr_mcbond_it2.782.9961758
X-RAY DIFFRACTIONr_mcbond_other2.7762.9941757
X-RAY DIFFRACTIONr_mcangle_it3.854.472222
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 125 -
Rwork0.274 2455 -
all-2580 -
obs--98.96 %

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