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- PDB-3zjn: M.acetivorans protoglobin in complex with cyanide -

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Basic information

Entry
Database: PDB / ID: 3zjn
TitleM.acetivorans protoglobin in complex with cyanide
ComponentsPROTOGLOBIN
KeywordsIRON-BINDING PROTEIN / CYANIDE COMPLEX
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Globin-sensor domain-containing protein
Similarity search - Component
Biological speciesMETHANOSARCINA ACETIVORANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)47,86212
Polymers46,0222
Non-polymers1,84010
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-76.3 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.150, 47.960, 80.290
Angle α, β, γ (deg.)90.00, 106.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 453 molecules

#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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.97 Å3/Da / Density % sol: 37.56 % / Description: NONE
Crystal growpH: 7
Details: 20% PEG 4000, 10% ISOPROPANOL, 0.1 M HEPES PH 7.0, 0.02 M POTASSIUM FERRICYANIDE, 0.01 M KCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→26.32 Å / Num. obs: 44547 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEB

2veb


Resolution: 1.6→25.84 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.333 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23831 2238 5.1 %RANDOM
Rwork0.17485 ---
obs0.17808 41953 93.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.03 Å2
2---0.06 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 125 443 3759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6052.0284857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03223.708178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35115566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4711519
X-RAY DIFFRACTIONr_chiral_restr0.1210.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212765
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_it1.4111.51960
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1923201
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.36831576
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8084.51639
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.72133536
X-RAY DIFFRACTIONr_sphericity_free11.9373466
X-RAY DIFFRACTIONr_sphericity_bonded6.19433407
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 166 -
Rwork0.191 2919 -
obs--89.37 %

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