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- PDB-3qzx: 3D Structure of ferric methanosarcina acetivorans protoglobin Y61... -

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Basic information

Entry
Database: PDB / ID: 3qzx
Title3D Structure of ferric methanosarcina acetivorans protoglobin Y61A mutant with unknown ligand
ComponentsMethanosarcina acetivorans protoglobin
KeywordsOXYGEN BINDING / OXYGEN TRANSPORT / globin fold / protoglobin / METHANOGENESIS / ARCHAEA 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 / PHOSPHATE ION / Globin-sensor domain-containing protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPesce, A. / Tilleman, L. / Dewilde, S. / Ascenzi, P. / Coletta, M. / Ciaccio, C. / Bruno, S. / Moens, L. / Bolognesi, M. / Nardini, M.
Citation
Journal: Iubmb Life / Year: 2011
Title: Structural heterogeneity and ligand gating in ferric methanosarcina acetivorans protoglobin mutants.
Authors: Pesce, A. / Tilleman, L. / Dewilde, S. / Ascenzi, P. / Coletta, M. / Ciaccio, C. / Bruno, S. / Moens, L. / Bolognesi, M. / Nardini, M.
#1: Journal: EMBO Rep. / Year: 2008
Title: Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity
Authors: Nardini, M. / Pesce, A. / Thijs, L. / Saito, J.A. / Dewilde, S. / Alam, M. / Ascenzi, P. / Coletta, M. / Ciaccio, C. / Moens, L. / Bolognesi, M.
History
DepositionMar 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Methanosarcina acetivorans protoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8175
Polymers22,9191
Non-polymers8994
Water4,594255
1
A: Methanosarcina acetivorans protoglobin
hetero molecules

A: Methanosarcina acetivorans protoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,63510
Polymers45,8382
Non-polymers1,7978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7510 Å2
ΔGint-96 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.089, 49.239, 51.514
Angle α, β, γ (deg.)90.00, 92.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

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Components

#1: Protein Methanosarcina acetivorans protoglobin


Mass: 22918.768 Da / Num. of mol.: 1 / Mutation: Y61A, C101S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: MA_2883 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TLY9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.4 monobasic ammonium phosphate, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.3→51.43 Å / Num. obs: 49084 / % possible obs: 99.6 %
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→41.93 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.273 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16399 2482 5.1 %RANDOM
Rwork0.13203 ---
obs0.13364 46601 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.739 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.02 Å2
2---0.12 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 59 255 1898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221797
X-RAY DIFFRACTIONr_angle_refined_deg1.3392.0232474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5775210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95923.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54815288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.495159
X-RAY DIFFRACTIONr_chiral_restr0.3310.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211409
X-RAY DIFFRACTIONr_mcbond_it2.5631.5997
X-RAY DIFFRACTIONr_mcangle_it3.60621630
X-RAY DIFFRACTIONr_scbond_it4.9453800
X-RAY DIFFRACTIONr_scangle_it6.5334.5834
X-RAY DIFFRACTIONr_rigid_bond_restr3.15231797
X-RAY DIFFRACTIONr_sphericity_free15.4913260
X-RAY DIFFRACTIONr_sphericity_bonded9.03231730
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 182 -
Rwork0.229 3452 -
obs--99.73 %

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