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- PDB-8oup: Structural characterization of the hexa-coordinated globin from S... -

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Basic information

Entry
Database: PDB / ID: 8oup
TitleStructural characterization of the hexa-coordinated globin from Spisula solidissima
ComponentsNerve hemoglobin
KeywordsOXYGEN BINDING / Nerve hemoglobins / heme hexa-coordination / dimeric hemoglobins
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / heme binding / extracellular region / metal ion binding
Similarity search - Function
Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Nerve hemoglobin
Similarity search - Component
Biological speciesSpisula solidissima (Atlantic surf clam)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNardini, M. / Pesce, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117646RB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesCEX2021-001202-M Spain
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Structural and dynamic characterization of the hexa-coordinated globin from Spisula solidissima.
Authors: Pesce, A. / Barmpidi, K. / Dewilde, S. / Estarellas, C. / Moens, L. / Bolognesi, M. / Luque, F.J. / Nardini, M.
History
DepositionApr 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nerve hemoglobin
B: Nerve hemoglobin
C: Nerve hemoglobin
D: Nerve hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,22212
Polymers73,3884
Non-polymers2,8348
Water16,358908
1
A: Nerve hemoglobin
B: Nerve hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2958
Polymers36,6942
Non-polymers1,6016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-46 kcal/mol
Surface area14090 Å2
MethodPISA
2
C: Nerve hemoglobin
D: Nerve hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9274
Polymers36,6942
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-42 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.219, 50.684, 74.165
Angle α, β, γ (deg.)75.65, 88.09, 85.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nerve hemoglobin


Mass: 18347.010 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spisula solidissima (Atlantic surf clam)
Gene: nHb
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q3MQ26
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.5 M ammonium sulfate, and 50 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→49.01 Å / Num. obs: 70881 / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 24.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 11.9 / Num. unique obs: 10388 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→49.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.732 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19685 3579 5 %RANDOM
Rwork0.14981 ---
obs0.1522 67301 94.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.11 Å2-0.63 Å2
2---0.27 Å2-0.24 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4875 0 196 908 5979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125449
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165035
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.6947456
X-RAY DIFFRACTIONr_angle_other_deg0.6081.60311730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7615667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.6771021
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61510962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026173
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021189
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_it1.9231.5642484
X-RAY DIFFRACTIONr_mcbond_other1.9211.5642484
X-RAY DIFFRACTIONr_mcangle_it2.9732.3313117
X-RAY DIFFRACTIONr_mcangle_other2.9732.3323118
X-RAY DIFFRACTIONr_scbond_it2.7071.8442965
X-RAY DIFFRACTIONr_scbond_other2.7071.8452966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1292.634307
X-RAY DIFFRACTIONr_long_range_B_refined6.41528.7027258
X-RAY DIFFRACTIONr_long_range_B_other6.00323.6626912
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 251 -
Rwork0.162 5000 -
obs--94.72 %

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