[English] 日本語
Yorodumi
- PDB-4ncq: Crystal structure of NiSOD H1A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ncq
TitleCrystal structure of NiSOD H1A mutant
ComponentsSuperoxide dismutase [Ni]
KeywordsOXIDOREDUCTASE / antioxidant / hexamer / superoxide dismutase / NiSOD / SOD / metal-binding / Ni-binding / Ni
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / nickel cation binding / cytoplasm
Similarity search - Function
Nickel-containing superoxide dismutase / Superoxide dismutase, Nickel-type / Nickel-containing superoxide dismutase superfamily / Nickel-containing superoxide dismutase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Superoxide dismutase [Ni]
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 Å
AuthorsGuce, A.I. / Garman, S.C.
CitationJournal: Biochemistry / Year: 2015
Title: Nickel superoxide dismutase: structural and functional roles of His1 and its H-bonding network.
Authors: Ryan, K.C. / Guce, A.I. / Johnson, O.E. / Brunold, T.C. / Cabelli, D.E. / Garman, S.C. / Maroney, M.J.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]


Theoretical massNumber of molelcules
Total (without water)39,4683
Polymers39,4683
Non-polymers00
Water3,243180
1
A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]

A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]


Theoretical massNumber of molelcules
Total (without water)78,9356
Polymers78,9356
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10350 Å2
ΔGint-54 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.950, 110.742, 111.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

21C-232-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALALAALA1AA8 - 148 - 14
21VALVALALAALA1BB8 - 148 - 14
31VALVALALAALA1CC8 - 148 - 14
12ARGARGARGARG2AA1515
22ARGARGARGARG2BB1515
32ARGARGARGARG2CC1515
13ILEILEGLNGLN1AA16 - 2516 - 25
23ILEILEGLNGLN1BB16 - 2516 - 25
33ILEILEGLNGLN1CC16 - 2516 - 25
14GLUGLULYSLYS2AA26 - 2726 - 27
24GLUGLULYSLYS2BB26 - 2726 - 27
34GLUGLULYSLYS2CC26 - 2726 - 27
15METMETMETMET1AA2828
25METMETMETMET1BB2828
35METMETMETMET1CC2828
16ALAALAPHEPHE4AA29 - 3629 - 36
26ALAALAPHEPHE4BB29 - 3629 - 36
36ALAALAPHEPHE4CC29 - 3629 - 36
17GLNGLNPHEPHE1AA37 - 6337 - 63
27GLNGLNPHEPHE1BB37 - 6337 - 63
37GLNGLNPHEPHE1CC37 - 6337 - 63
18LYSLYSLYSLYS3AA6464
28LYSLYSLYSLYS3BB6464
38LYSLYSLYSLYS3CC6464
19PROPROSERSER1AA65 - 9165 - 91
29PROPROSERSER1BB65 - 9165 - 91
39PROPROSERSER1CC65 - 9165 - 91
110LYSLYSTHRTHR4AA92 - 9692 - 96
210LYSLYSTHRTHR4BB92 - 9692 - 96
310LYSLYSTHRTHR4CC92 - 9692 - 96
111GLYGLYGLYGLY1AA9797
211GLYGLYGLYGLY1BB9797
311GLYGLYGLYGLY1CC9797
112GLNGLNLYSLYS4AA98 - 9998 - 99
212GLNGLNLYSLYS4BB98 - 9998 - 99
312GLNGLNLYSLYS4CC98 - 9998 - 99
113ALAALATRPTRP1AA100 - 112100 - 112
213ALAALATRPTRP1BB100 - 112100 - 112
313ALAALATRPTRP1CC100 - 112100 - 112
114GLUGLULYSLYS4AA113 - 116113 - 116
214GLUGLULYSLYS4BB113 - 116113 - 116
314GLUGLULYSLYS4CC113 - 116113 - 116

-
Components

#1: Protein Superoxide dismutase [Ni] / NiSOD / Nickel-containing superoxide dismutase


Mass: 13155.896 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 15-131 / Mutation: H1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: 2SC7G11.16c, SCO5254, sod1, sodN / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P80735, superoxide dismutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 550 MME, 0.05 M CaCl2, 0.1 M Bis-Tris, pH 6.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9184 Å
DetectorType: ADSC / Detector: CCD / Date: Aug 15, 2007 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 20104 / Num. obs: 20104 / % possible obs: 89.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Χ2: 1.137 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.07-2.144.40.64820100.909190.8
2.14-2.234.40.5220071.274190.6
2.23-2.334.40.42319841.157189.7
2.33-2.454.40.3319791.03189
2.45-2.614.30.23719581.103188.1
2.61-2.814.30.1719421.395187.2
2.81-3.094.30.11419211.43185.6
3.09-3.544.30.06919301.419185.4
3.54-4.464.10.04920040.64187.9
4.46-504.70.03423691.044199.3

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB 3GX4

3gx4


Resolution: 2.08→30.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.954 / SU ML: 0.146 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 996 5 %RANDOM
Rwork0.1847 ---
obs0.1871 20025 88.43 %-
all-20025 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.17 Å2 / Biso mean: 46.4279 Å2 / Biso min: 27.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2---0.33 Å20 Å2
3---2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.08→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 0 180 2827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192713
X-RAY DIFFRACTIONr_bond_other_d0.0010.022595
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.9433670
X-RAY DIFFRACTIONr_angle_other_deg0.72436007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0245327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4525.116129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12215481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.527159
X-RAY DIFFRACTIONr_chiral_restr0.0540.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A332MEDIUM POSITIONAL0.6512
2B332MEDIUM POSITIONAL0.6312
3C332MEDIUM POSITIONAL0.7512
1A16LOOSE POSITIONAL0.9818
2B16LOOSE POSITIONAL0.6818
3C16LOOSE POSITIONAL0.818
1A1387TIGHT THERMAL2.670.5
2B1387TIGHT THERMAL2.630.5
3C1387TIGHT THERMAL2.480.5
1A332MEDIUM THERMAL5.012
2B332MEDIUM THERMAL3.732
3C332MEDIUM THERMAL4.492
1A16LOOSE THERMAL3.6710
2B16LOOSE THERMAL4.8910
3C16LOOSE THERMAL3.9510
LS refinement shellResolution: 2.084→2.138 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 71 -
Rwork0.255 1294 -
all-1365 -
obs--82.73 %
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)
13.9195-1.8426-0.06051.8510.42050.64750.0365-0.00090.2486-0.09920.0076-0.0987-0.07050.0264-0.04410.09050.00770.0360.01570.02720.08170.66824.20116.712
22.03491.3586-1.18581.5907-0.89382.0807-0.11740.2496-0.0391-0.06530.08980.05730.0808-0.12480.02760.07040.01480.00290.0541-0.01460.01120.917-7.69116.399
31.2443-0.6438-1.22871.22890.98173.16830.0295-0.0630.01210.1427-0.0107-0.07070.12180.0644-0.01870.0505-0.0264-0.04250.04290.03190.065615.7118.32939.894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 117
2X-RAY DIFFRACTION2B8 - 116
3X-RAY DIFFRACTION3C8 - 116

+
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://pdbjlvh1.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