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- PDB-3gkt: Crystal structure of murine neuroglobin under Kr pressure -

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Basic information

Entry
Database: PDB / ID: 3gkt
TitleCrystal structure of murine neuroglobin under Kr pressure
ComponentsNeuroglobin
KeywordsOXYGEN STORAGE/TRANSPORT PROTEIN / Ngb / neuroglobin / Krypton / OXYGEN STORAGE-TRANSPORT PROTEIN COMPLEX / Heme / Iron / Metal-binding / Oxygen transport / Transport
Function / homology
Function and homology information


Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hydrogen peroxide / neuron projection development / cellular response to hypoxia ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hydrogen peroxide / neuron projection development / cellular response to hypoxia / perikaryon / response to hypoxia / mitochondrial matrix / heme binding / negative regulation of apoptotic process / metal ion binding / cytosol
Similarity search - Function
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 / KRYPTON / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.86 Å
AuthorsMoschetti, T. / Mueller, U. / Schultze, J. / Brunori, M. / Vallone, B.
CitationJournal: Biophys. J. / Year: 2009
Title: The structure of neuroglobin at high Xe and Kr pressure reveals partial conservation of globin internal cavities.
Authors: Moschetti, T. / Mueller, U. / Schulze, J. / Brunori, M. / Vallone, B.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,1875
Polymers17,3071
Non-polymers8804
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neuroglobin
hetero molecules

A: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,37310
Polymers34,6132
Non-polymers1,7608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area4760 Å2
ΔGint-90 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.800, 88.800, 113.500
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-210-

HOH

21A-217-

HOH

31A-224-

HOH

41A-225-

HOH

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Components

#1: Protein Neuroglobin


Mass: 17306.572 Da / Num. of mol.: 1 / Mutation: C55S, C120S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9ER97
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Kr
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulphate, 0.1M MES, pH6.5, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.86437 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86437 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. obs: 14316 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.17 % / Biso Wilson estimate: 35.127 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.86→2.1 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.03 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1Q1F

1q1f


Resolution: 1.86→19.55 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.186 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20839 716 5 %RANDOM
Rwork0.17275 ---
all0.256 14315 --
obs0.17451 13599 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.535 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å20 Å2
2---0.25 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.86→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1149 0 50 75 1274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221342
X-RAY DIFFRACTIONr_angle_refined_deg1.4522.1711867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5395166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3192350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73115211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.071158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021029
X-RAY DIFFRACTIONr_nbd_refined0.2180.2647
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2906
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.280
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.220
X-RAY DIFFRACTIONr_mcbond_it0.7611.5773
X-RAY DIFFRACTIONr_mcangle_it1.28321257
X-RAY DIFFRACTIONr_scbond_it2.0333638
X-RAY DIFFRACTIONr_scangle_it2.8074.5597
LS refinement shellResolution: 1.864→1.912 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 40 -
Rwork0.21 759 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
117.66294.8615-3.27936.3058-26.958727.23840.7045-0.8625-1.27880.4925-1.2365-0.99410.8861.61010.5320.0030.0842-0.0698-0.04440.1150.168627.3135.25933.151
26.6906-0.9887-1.47364.52850.1912.7709-0.0038-0.20390.18470.1632-0.0187-0.3181-0.07650.0550.0225-0.048-0.0264-0.071-0.0058-0.004-0.110514.44553.86427.006
34.5954-0.79751.09862.9979-1.24982.77480.1965-0.304-0.09110.3783-0.2126-0.4925-0.01180.19780.0161-0.0429-0.0696-0.1186-0.0107-0.0147-0.038321.22452.48931.671
41.65230.82340.01911.6073-1.05562.07630.3215-0.4348-0.05760.5357-0.267-0.2664-0.2356-0.0493-0.05450.0849-0.0923-0.10740.08270.0455-0.022715.37548.0936.834
53.705-1.4727-2.873418.88556.40338.39980.0171-0.6657-0.26171.0451-0.44550.29570.06980.33640.42840.0728-0.1111-0.14690.06870.1706-0.021515.98941.55740.963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 17
2X-RAY DIFFRACTION2A18 - 47
3X-RAY DIFFRACTION3A48 - 85
4X-RAY DIFFRACTION4A86 - 124
5X-RAY DIFFRACTION5A125 - 150

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