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- PDB-2vry: Mouse Neuroglobin with heme iron in the reduced ferrous state -

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Basic information

Entry
Database: PDB / ID: 2vry
TitleMouse Neuroglobin with heme iron in the reduced ferrous state
ComponentsNEUROGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX / METAL- BINDING / PHOTOREDUCTION / OXYGEN TRANSPORT / IRON / HEME / FERROUS / TRANSPORT / NEUROGLOBIN / GLOBIN FOLD / HEME PROTEIN / METAL-BINDING
Function / homology
Function and homology information


Intracellular oxygen transport / positive regulation of catalytic activity / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / neuron projection development / cellular response to hydrogen peroxide ...Intracellular oxygen transport / positive regulation of catalytic activity / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / neuron projection development / cellular response to hydrogen peroxide / cellular response to hypoxia / response to hypoxia / perikaryon / mitochondrial matrix / heme binding / negative regulation of apoptotic process / cytosol
Similarity search - Function
: / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsArcovito, A. / Moschetti, T. / D'Angelo, P. / Mancini, G. / Vallone, B. / Brunori, M. / Della Longa, S.
CitationJournal: Arch.Biochem.Biophys. / Year: 2008
Title: An X-Ray Diffraction and X-Ray Absorption Spectroscopy Joint Study of Neuroglobin.
Authors: Arcovito, A. / Moschetti, T. / D'Angelo, P. / Mancini, G. / Vallone, B. / Brunori, M. / Della Longa, S.
History
DepositionApr 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.5Sep 2, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_label_alt_id ..._pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1154
Polymers17,3071
Non-polymers8093
Water1,33374
1
A: NEUROGLOBIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)108,69124
Polymers103,8396
Non-polymers4,85218
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area12800 Å2
ΔGint-32.7 kcal/mol
Surface area44690 Å2
MethodPQS
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.920, 87.920, 113.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

21A-2009-

HOH

31A-2035-

HOH

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Components

#1: Protein NEUROGLOBIN


Mass: 17306.572 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CONTAINS THREE ADDITIONAL AMINO ACIDS AT THE N TERM GLY, SER, HIS
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: FVB/N / Cell: NEURONS / Organ: BRAIN / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q9ER97
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 55 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 120 TO SER
Has protein modificationY
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THE HEME IRON IS IN THE REDUCED FERROUS STATE

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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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6.5
Details: 1.6 M AMMONIUM SULFATE, 0.1 MMES, PH 6.5, 10% V/V DIOXANE, 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 12881 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7
Reflection shellResolution: 1.93→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q1F

1q1f


Resolution: 1.87→63.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.392 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE OF UNLIGANDED NEUROGLOBIN, WITH REDUCED HEME IRON STATE (FERROUS).
RfactorNum. reflection% reflectionSelection details
Rfree0.217 692 5 %RANDOM
Rwork0.185 ---
obs0.187 13093 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.87→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1134 0 53 74 1261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221308
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5212.1751814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5745155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94822.97947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46515203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.175157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02984
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2896
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4490.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8421.5768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39321220
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1683628
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9474.5585
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: 1.87→1.92 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 55
Rwork0.214 746
Refinement TLS params.Method: refined / Origin x: 17.722 Å / Origin y: 47.406 Å / Origin z: 33.543 Å
111213212223313233
T-0.017 Å2-0.0439 Å2-0.111 Å2--0.0399 Å20.0294 Å2---0.0028 Å2
L1.4932 °20.3525 °20.0345 °2-3.0479 °2-0.5283 °2--2.0052 °2
S0.1193 Å °-0.1752 Å °-0.1993 Å °0.4991 Å °-0.1752 Å °-0.4767 Å °0.0952 Å °0.0764 Å °0.0559 Å °

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