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- PDB-7vqg: The X-ray structure of human neuroglobin A15C mutant -

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Basic information

Entry
Database: PDB / ID: 7vqg
TitleThe X-ray structure of human neuroglobin A15C mutant
ComponentsNeuroglobin
KeywordsOXYGEN BINDING / 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
1,4-DIETHYLENE DIOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLin, Y.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The X-ray structure of human neuroglobin A15C mutant
Authors: Lin, Y.W.
History
DepositionOct 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9348
Polymers16,6661
Non-polymers1,2687
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-20 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.093, 40.561, 84.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-351-

HOH

31A-423-

HOH

41A-430-

HOH

51A-437-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuroglobin


Mass: 16666.076 Da / Num. of mol.: 1 / Mutation: A15C
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

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Non-polymers , 5 types, 163 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% v/v 1,4-Dioxane, 0.1 M MES monohydrate pH 6.5, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.35→36.58 Å / Num. obs: 60134 / % possible obs: 99.66 % / Redundancy: 12.4 % / Biso Wilson estimate: 14.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.012 / Net I/σ(I): 37.83
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 10.86 / Num. unique obs: 5676 / CC1/2: 0.994 / Rpim(I) all: 0.151 / % possible all: 96.57

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OJ6

1oj6


Resolution: 1.35→36.58 Å / SU ML: 0.092 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.5388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.172 2857 5.04 %
Rwork0.1439 53791 -
obs0.1454 56648 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.32 Å2
Refinement stepCycle: LAST / Resolution: 1.35→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 83 156 1401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01841319
X-RAY DIFFRACTIONf_angle_d1.67461807
X-RAY DIFFRACTIONf_chiral_restr0.1028187
X-RAY DIFFRACTIONf_plane_restr0.011224
X-RAY DIFFRACTIONf_dihedral_angle_d22.7342487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.24311290.14832550X-RAY DIFFRACTION93.97
1.37-1.40.19831350.13892666X-RAY DIFFRACTION98.04
1.4-1.430.20141360.12962642X-RAY DIFFRACTION98.51
1.43-1.450.17711510.12442718X-RAY DIFFRACTION98.86
1.45-1.490.15791380.11642671X-RAY DIFFRACTION98.98
1.49-1.520.15191470.11162695X-RAY DIFFRACTION99.51
1.52-1.560.16121340.11162729X-RAY DIFFRACTION99.58
1.56-1.60.15831420.11412668X-RAY DIFFRACTION99.15
1.6-1.650.15411500.11712672X-RAY DIFFRACTION99.54
1.65-1.70.16621570.11952752X-RAY DIFFRACTION99.62
1.7-1.760.18641370.12512705X-RAY DIFFRACTION99.82
1.76-1.830.19071460.12932677X-RAY DIFFRACTION99.75
1.83-1.920.16591290.13132716X-RAY DIFFRACTION99.75
1.92-2.020.16761390.13392704X-RAY DIFFRACTION99.75
2.02-2.140.19531540.1312702X-RAY DIFFRACTION99.86
2.14-2.310.19221400.13332723X-RAY DIFFRACTION99.86
2.31-2.540.13451550.13582692X-RAY DIFFRACTION99.75
2.54-2.910.14311450.14892703X-RAY DIFFRACTION99.82
2.91-3.660.1751490.16012702X-RAY DIFFRACTION99.79
3.66-36.580.18881440.17522704X-RAY DIFFRACTION99.62

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