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- PDB-3zjr: M.acetivorans protoglobin in complex with cyanide and Xenon -

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Basic information

Entry
Database: PDB / ID: 3zjr
TitleM.acetivorans protoglobin in complex with cyanide and Xenon
ComponentsPROTOGLOBIN
KeywordsIRON-BINDING PROTEIN / CYANIDE-XENON 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 / XENON / Globin-sensor domain-containing protein
Similarity search - Component
Biological speciesMETHANOSARCINA ACETIVORANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7854
Polymers23,0111
Non-polymers7743
Water39622
1
A: PROTOGLOBIN
hetero molecules

A: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5698
Polymers46,0222
Non-polymers1,5486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6730 Å2
ΔGint-74.3 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.498, 50.169, 51.389
Angle α, β, γ (deg.)90.00, 100.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTOGLOBIN


Mass: 23010.863 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.22 Å3/Da / Density % sol: 44.56 % / 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: 3→50.64 Å / Num. obs: 3627 / % possible obs: 87.8 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.3 / % possible all: 91.3

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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: 3→42.37 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.862 / SU B: 25.319 / SU ML: 0.433 / Cross valid method: THROUGHOUT / ESU R Free: 0.679 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FINAL STRUCTURE HAS NO RESIDUES IN THE DISALLOWED REGION OF RAMACHANDRAN PLOT AS DEFINED IN THE CCP4 PROCHECK PROGRAM.
RfactorNum. reflection% reflectionSelection details
Rfree0.30621 160 4.4 %RANDOM
Rwork0.2041 ---
obs0.20825 3449 87.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.786 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.03 Å2
2--0.57 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 3→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 46 22 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221703
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4262.0232331
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25923.67887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.86415266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.335159
X-RAY DIFFRACTIONr_chiral_restr0.090.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211343
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_it0.5451.5955
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02221546
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9963748
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7854.5784
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 14 -
Rwork0.345 241 -
obs--89.47 %

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