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- PDB-3zjq: M.acetivorans protoglobin in complex with nicotinamide -

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Basic information

Entry
Database: PDB / ID: 3zjq
TitleM.acetivorans protoglobin in complex with nicotinamide
ComponentsPROTOGLOBIN
KeywordsIRON-BINDING PROTEIN
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding
Similarity search - Function
Protoglobin / Globin-sensor domain / Protoglobin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NICOTINAMIDE / Globin-sensor domain-containing protein
Similarity search - Component
Biological speciesMETHANOSARCINA ACETIVORANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPesce, A. / Tilleman, L. / Donne, J. / Aste, E. / Ascenzi, P. / Ciaccio, C. / Coletta, M. / Moens, L. / Viappiani, C. / Dewilde, S. ...Pesce, A. / Tilleman, L. / Donne, J. / Aste, E. / Ascenzi, P. / Ciaccio, C. / Coletta, M. / Moens, L. / Viappiani, C. / Dewilde, S. / Bolognesi, M. / Nardini, M.
CitationJournal: Plos One / Year: 2013
Title: Structure and Haem-Distal Site Plasticity in Methanosarcina Acetivorans Protoglobin.
Authors: Pesce, A. / Tilleman, L. / Donne, J. / Aste, E. / Ascenzi, P. / Ciaccio, C. / Coletta, M. / Moens, L. / Viappiani, C. / Dewilde, S. / Bolognesi, M. / Nardini, M.
History
DepositionJan 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references / Structure summary
Revision 1.2Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_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 / _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: PROTOGLOBIN
B: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5917
Polymers46,0222
Non-polymers1,5695
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-74 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.530, 48.210, 81.010
Angle α, β, γ (deg.)90.00, 102.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTOGLOBIN


Mass: 23010.863 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA ACETIVORANS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8TLY9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC101S MUTATED FOR CRYSTALLIZATION PURPOSES

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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: 2.09 Å3/Da / Density % sol: 41.18 % / Description: NONE
Crystal growpH: 7.5
Details: 18% PEG 4000, 10% ISOPROPANOL, 0.1 M HEPES PH 7.5, 0.01 M POTASSIUM FERRICYANIDE, 0.04 M NICOTINAMIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.28 Å / Num. obs: 30234 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEB

2veb


Resolution: 1.9→79.01 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.087 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21138 1531 5.1 %RANDOM
Rwork0.17653 ---
obs0.17836 28690 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.138 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.53 Å2
2--0.08 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→79.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 110 311 3612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0622.0294719
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.785389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92823.6175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05915544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4341520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212724
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_it0.411.51920
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8223116
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32531527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2484.51598
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 123 -
Rwork0.212 2119 -
obs--100 %

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