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- PDB-4b4y: crystal structure of the neuroglobin from the photosymbiotic mari... -

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Basic information

Entry
Database: PDB / ID: 4b4y
Titlecrystal structure of the neuroglobin from the photosymbiotic marine acoel Symsagittifera roscoffensis
ComponentsNEUROGLOBIN
KeywordsTRANSPORT PROTEIN / NERVOUS SYSTEM EVOLUTION / GLOBIN EVOLUTION / CNIDARIAN / METAZOAN
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / metal ion binding
Similarity search - Function
: / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Neuroglobin
Similarity search - Component
Biological speciesSYMSAGITTIFERA ROSCOFFENSIS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLechauve, C. / Jager, M. / Laguerre, L. / Kiger, L. / Correc, G. / Leroux, C. / Vinogradov, S. / Czjzek, M. / Marden, M.C. / Bailly, X.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Neuroglobins: Pivotal Proteins Associated with Emerging Neural Systems and Precursors of Metazoan Globin Diversity.
Authors: Lechauve, C. / Jager, M. / Laguerre, L. / Kiger, L. / Correc, G. / Leroux, C. / Vinogradov, S. / Czjzek, M. / Marden, M.C. / Bailly, X.
History
DepositionAug 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Apr 29, 2015Group: Data collection
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Assembly

Deposited unit
A: NEUROGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1293
Polymers17,4801
Non-polymers6482
Water1,76598
1
A: NEUROGLOBIN
hetero molecules

A: NEUROGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2576
Polymers34,9602
Non-polymers1,2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area4080 Å2
ΔGint-47.2 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.070, 97.070, 140.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein NEUROGLOBIN


Mass: 17480.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYMSAGITTIFERA ROSCOFFENSIS (invertebrata)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7MTK4*PLUS
#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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 4.9 Å3/Da / Density % sol: 74.9 % / Description: NONE
Crystal growpH: 7.5
Details: 32% PEG 6000, 1.0 M LICL AND 0.1 M NA ACETATE, pH 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID23-110.933
SYNCHROTRONESRF BM30A21.7387
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 2, 2009
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
21.73871
ReflectionResolution: 2.3→2.36 Å / Num. obs: 20104 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / % possible all: 77.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→30.06 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.224 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25084 904 5.1 %RANDOM
Rwork0.21464 ---
obs0.2165 16886 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.064 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.25 Å20 Å2
2---0.51 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 45 98 1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4582.0641729
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75125.84953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97415237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.724153
X-RAY DIFFRACTIONr_chiral_restr0.1650.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021937
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_it1.4371.5749
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.58821216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0463522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0364.5511
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 73 -
Rwork0.305 1201 -
obs--98.76 %

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