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- PDB-8wub: The X-ray structure of human neuroglobin C120S mutant -

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Basic information

Entry
Database: PDB / ID: 8wub
TitleThe X-ray structure of human neuroglobin C120S mutant
ComponentsNeuroglobin
KeywordsOXYGEN TRANSPORT / 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: 1.5 Å
AuthorsLin, Y.W. / Yuan, H.
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 C120S mutant
Authors: Lin, Y.W. / Yuan, H.
History
DepositionOct 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuroglobin
B: Neuroglobin
C: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,23212
Polymers50,8063
Non-polymers2,4269
Water8,035446
1
A: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7444
Polymers16,9351
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8405
Polymers16,9351
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6483
Polymers16,9351
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.009, 119.940, 38.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 16 or resid 18...
d_2ens_1(chain "B" and (resid 4 through 16 or resid 18...
d_3ens_1(chain "C" and (resid 4 through 16 or resid 18...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROVALVALAA4 - 164 - 16
d_12ARGARGASNASNAA18 - 4518 - 45
d_13ARGARGASPASPAA47 - 5447 - 54
d_14LEULEUVALVALAA56 - 7156 - 71
d_15ASPASPSERSERAA73 - 8373 - 83
d_16LEULEUALAALAAA85 - 9085 - 90
d_17LEULEUPHEPHEAA92 - 10692 - 106
d_18THRTHRTYRTYRAA108 - 115108 - 115
d_19LEULEUGLUGLUAA117 - 118117 - 118
d_110SERSERTHRTHRAA120 - 129120 - 129
d_111ALAALATRPTRPAA131 - 133131 - 133
d_112LEULEUMETMETAA136 - 144136 - 144
d_113ARGARGTRPTRPAA146 - 148146 - 148
d_114HEMHEMHEMHEMAD201
d_21PROPROVALVALBB4 - 164 - 16
d_22ARGARGASNASNBB18 - 4518 - 45
d_23ARGARGASPASPBB47 - 5447 - 54
d_24LEULEUVALVALBB56 - 7156 - 71
d_25ASPASPSERSERBB73 - 8373 - 83
d_26LEULEUALAALABB85 - 9085 - 90
d_27LEULEUPHEPHEBB92 - 10692 - 106
d_28THRTHRTYRTYRBB108 - 115108 - 115
d_29LEULEUGLUGLUBB117 - 118117 - 118
d_210SERSERTHRTHRBB120 - 129120 - 129
d_211ALAALATRPTRPBB131 - 133131 - 133
d_212LEULEUMETMETBB136 - 144136 - 144
d_213ARGARGTRPTRPBB146 - 148146 - 148
d_214HEMHEMHEMHEMBG201
d_31PROPROVALVALCC4 - 164 - 16
d_32ARGARGASNASNCC18 - 4518 - 45
d_33ARGARGASPASPCC47 - 5447 - 54
d_34LEULEUVALVALCC56 - 7156 - 71
d_35ASPASPSERSERCC73 - 8373 - 83
d_36LEULEUALAALACC85 - 9085 - 90
d_37LEULEUPHEPHECC92 - 10692 - 106
d_38THRTHRTYRTYRCC108 - 115108 - 115
d_39LEULEUGLUGLUCC117 - 118117 - 118
d_310SERSERTHRTHRCC120 - 129120 - 129
d_311ALAALATRPTRPCC131 - 133131 - 133
d_312LEULEUMETMETCC136 - 144136 - 144
d_313ARGARGTRPTRPCC146 - 148146 - 148
d_314HEMHEMHEMHEMCK201

NCS oper:
IDCodeMatrixVector
1given(-0.997799501793, 0.0656270627263, 0.00944684385406), (-0.0656833016059, -0.997823831438, -0.00577107485329), (0.00904754723805, -0.00637887550751, 0.999938724041)-0.370173942223, 38.3920393764, 0.401957831033
2given(-0.994591202342, 0.103121195305, 0.0124241419198), (-0.103039940299, -0.994652493303, 0.00701343494522), (0.0130809375325, 0.00569531785303, 0.999898221034)-2.75278696558, 77.6939572153, 0.338753114064

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Components

#1: Protein Neuroglobin


Mass: 16935.307 Da / Num. of mol.: 3 / Mutation: C120S
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.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 1.93 Å3/Da / Density % sol: 36.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.6 M ammonium sulfate,10% v/v 1,4-Dioxane, 0.1 M MES monohydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 63053 / % possible obs: 98.73 % / Redundancy: 9 % / Biso Wilson estimate: 17.85 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06813 / Rpim(I) all: 0.02429 / Net I/σ(I): 18.9
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.3732 / Mean I/σ(I) obs: 4.51 / Num. unique obs: 6260 / CC1/2: 0.983 / Rpim(I) all: 0.1406 / % possible all: 99.92

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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: 1.5→28.52 Å / SU ML: 0.1578 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.3928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2036 3194 5.07 %
Rwork0.1535 59822 -
obs0.1561 63016 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.06 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 159 447 4051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613893
X-RAY DIFFRACTIONf_angle_d1.52245362
X-RAY DIFFRACTIONf_chiral_restr0.0959563
X-RAY DIFFRACTIONf_plane_restr0.0105679
X-RAY DIFFRACTIONf_dihedral_angle_d24.29021412
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.635369555677
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.45061036929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.23471460.14372560X-RAY DIFFRACTION99.93
1.52-1.550.24971130.14312617X-RAY DIFFRACTION99.89
1.55-1.570.21151430.13872570X-RAY DIFFRACTION100
1.57-1.60.25441310.13822618X-RAY DIFFRACTION99.89
1.6-1.630.25771460.13842606X-RAY DIFFRACTION99.85
1.63-1.660.21091390.13932581X-RAY DIFFRACTION99.96
1.66-1.690.24951390.13352622X-RAY DIFFRACTION100
1.69-1.730.21331570.13472540X-RAY DIFFRACTION99.93
1.73-1.770.21511570.13162623X-RAY DIFFRACTION99.89
1.77-1.810.24631460.13852579X-RAY DIFFRACTION99.89
1.81-1.860.2251120.14342637X-RAY DIFFRACTION99.93
1.86-1.910.20451160.15432221X-RAY DIFFRACTION99.03
1.92-1.980.24131420.14282323X-RAY DIFFRACTION98.52
1.98-2.050.20911240.14082676X-RAY DIFFRACTION99.82
2.05-2.130.21681690.13792581X-RAY DIFFRACTION99.82
2.13-2.230.18341380.1342609X-RAY DIFFRACTION99.78
2.23-2.350.18361430.13732639X-RAY DIFFRACTION99.96
2.35-2.490.19371280.15052665X-RAY DIFFRACTION99.89
2.49-2.690.20891340.15522649X-RAY DIFFRACTION99.93
2.69-2.960.19651490.15382658X-RAY DIFFRACTION99.93
2.96-3.380.19491410.15542693X-RAY DIFFRACTION99.86
3.38-4.260.17591380.1452726X-RAY DIFFRACTION99.97
4.26-28.520.20621430.20392829X-RAY DIFFRACTION98.54

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