[English] 日本語
Yorodumi
- PDB-8wub: The X-ray structure of human neuroglobin C120S mutant -

+
Open data


ID or keywords:

Loading...

-
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 domain profile. / Globin / Globin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more