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- PDB-3zjm: Ile(149)G11Phe mutation of M.acetivorans protoglobin in complex w... -

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Basic information

Entry
Database: PDB / ID: 3zjm
TitleIle(149)G11Phe mutation of M.acetivorans protoglobin in complex with cyanide
ComponentsPROTOGLOBIN
KeywordsIRON-BINDING PROTEIN / HAEM-DISTAL SITE MUTATION
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 / Globin-sensor domain-containing protein
Similarity search - Component
Biological speciesMETHANOSARCINA ACETIVORANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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
C: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,81514
Polymers69,1353
Non-polymers2,68011
Water8,593477
1
C: PROTOGLOBIN
hetero molecules

C: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,22012
Polymers46,0902
Non-polymers2,13010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7930 Å2
ΔGint-71.3 kcal/mol
Surface area15640 Å2
MethodPISA
2
A: PROTOGLOBIN
B: PROTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7058
Polymers46,0902
Non-polymers1,6156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-67.5 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.720, 48.030, 98.680
Angle α, β, γ (deg.)90.00, 94.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2141-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein PROTOGLOBIN


Mass: 23044.879 Da / Num. of mol.: 3 / 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, 488 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsC101S MUTATED FOR CRYSTALLIZATION PURPOSES, I149F MUTATION

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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: 2.13 Å3/Da / Density % sol: 42.27 % / Description: NONE
Crystal growpH: 7.5
Details: 20% PEG 4000, 10% ISOPROPANOL, 0.1 M HEPES PH 7.5, 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: 1.5→26.14 Å / Num. obs: 92938 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3 / % possible all: 99.7

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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: 1.5→24.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.686 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22166 4654 5 %RANDOM
Rwork0.17774 ---
obs0.17996 88281 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.339 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.14 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4797 0 183 477 5457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5532.0267322
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88323.796274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40715833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9961529
X-RAY DIFFRACTIONr_chiral_restr0.1030.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214212
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_it1.4461.52961
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.26824823
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.17932364
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4754.52476
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.86335325
X-RAY DIFFRACTIONr_sphericity_free8.2433506
X-RAY DIFFRACTIONr_sphericity_bonded7.40835122
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 366 -
Rwork0.248 6434 -
obs--99.52 %

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