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- PDB-8grz: X-ray crystal structure of V71C human neuroglobin mutant -

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Basic information

Entry
Database: PDB / ID: 8grz
TitleX-ray crystal structure of V71C human neuroglobin mutant
ComponentsNeuroglobin
KeywordsOXYGEN STORAGE / human neuroglobin
Function / homology
Function and homology information


Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hypoxia / response to hypoxia / mitochondrial matrix ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hypoxia / response to hypoxia / mitochondrial matrix / heme binding / metal ion binding / cytosol
Similarity search - Function
: / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, Y.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: X-ray crystal structure of V71C human neuroglobin mutant
Authors: Lin, Y.W.
History
DepositionSep 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)17,5722
Polymers16,9551
Non-polymers6161
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-20 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.497, 39.553, 48.858
Angle α, β, γ (deg.)90.000, 120.318, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Neuroglobin


Mass: 16955.383 Da / Num. of mol.: 1 / Mutation: V71C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NGB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPG2
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9781 / % possible obs: 96.07 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.028 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.38 / Num. unique obs: 863 / CC1/2: 0.886 / Rpim(I) all: 0.235 / % possible all: 85.33

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MPM

4mpm


Resolution: 2→35.21 Å / SU ML: 0.185 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.5437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2342 560 5.73 %
Rwork0.2155 9205 -
obs0.2166 9765 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.82 Å2
Refinement stepCycle: LAST / Resolution: 2→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 43 60 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01461265
X-RAY DIFFRACTIONf_angle_d1.5491736
X-RAY DIFFRACTIONf_chiral_restr0.54184
X-RAY DIFFRACTIONf_plane_restr0.0128220
X-RAY DIFFRACTIONf_dihedral_angle_d26.7113457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.30811130.25382066X-RAY DIFFRACTION86.16
2.2-2.520.29881340.23632355X-RAY DIFFRACTION99.32
2.52-3.170.26721650.23342356X-RAY DIFFRACTION99.68
3.17-35.210.19261480.19652428X-RAY DIFFRACTION99.23

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