[English] 日本語
Yorodumi
- PDB-1xtl: Crystal structure of P104H mutant of SOD-like protein from Bacill... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xtl
TitleCrystal structure of P104H mutant of SOD-like protein from Bacillus subtilis.
ComponentsHypothetical superoxide dismutase-like protein yojM
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SOD / Cu-Zn SOD / SOD-like / superoxide dismutase mutants
Function / homology
Function and homology information


ion binding / superoxide dismutase activity / removal of superoxide radicals / copper ion binding / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Prokaryotic lipoprotein-attachment site / Prokaryotic lipoprotein-attachment site / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase-like protein YojM
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCalderone, V. / Mangani, S. / Banci, L. / Benvenuti, M. / Bertini, I. / Viezzoli, M.S. / Fantoni, A.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: From an Inactive Prokaryotic SOD Homologue to an Active Protein through Site-Directed Mutagenesis.
Authors: Banci, L. / Benvenuti, M. / Bertini, I. / Cabelli, D.E. / Calderone, V. / Fantoni, A. / Mangani, S. / Migliardi, M. / Viezzoli, M.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.
Authors: Banci, L. / Bertini, I. / Calderone, V. / Cramaro, F. / Del Conte, R. / Fantoni, A. / Mangani, S. / Quattrone, A. / Viezzoli, M.S.
History
DepositionOct 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Hypothetical superoxide dismutase-like protein yojM
A: Hypothetical superoxide dismutase-like protein yojM
C: Hypothetical superoxide dismutase-like protein yojM
D: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,02818
Polymers75,1194
Non-polymers90814
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical superoxide dismutase-like protein yojM
hetero molecules

C: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0149
Polymers37,5602
Non-polymers4547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1120 Å2
ΔGint-115 kcal/mol
Surface area14020 Å2
MethodPISA
3
A: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0405
Polymers18,7801
Non-polymers2604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0405
Polymers18,7801
Non-polymers2604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9744
Polymers18,7801
Non-polymers1943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
D: Hypothetical superoxide dismutase-like protein yojM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9744
Polymers18,7801
Non-polymers1943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.147, 56.586, 59.118
Angle α, β, γ (deg.)78.24, 89.91, 85.47
Int Tables number1
Space group name H-MP1
DetailsThe protein is a monomer in vivo but there are four molecules in the asymmetric unit

-
Components

#1: Protein
Hypothetical superoxide dismutase-like protein yojM


Mass: 18779.824 Da / Num. of mol.: 4 / Mutation: P83H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): TOP1 / References: UniProt: O31851
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na Acetate, 20% PEG4000, 0.1M Ammonium Sulphate, 10mM ZnCl2, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.3711 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 22, 2004 / Details: Double crystal focussing mono chromator
RadiationMonochromator: Double crystal focussing mono chromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3711 Å / Relative weight: 1
ReflectionResolution: 2→38.958 Å / Num. all: 41966 / Num. obs: 41966 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 28.733 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5985 / Rsym value: 0.244 / % possible all: 92.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S4I

1s4i


Resolution: 2→38.92 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.115 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.241 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29919 3477 8.3 %RANDOM
Rwork0.23186 ---
all0.23739 38482 --
obs0.23739 38482 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20.02 Å2-0.96 Å2
2--3.01 Å2-0.76 Å2
3----2.31 Å2
Refine analyzeLuzzati sigma a obs: 0.168 Å
Refinement stepCycle: LAST / Resolution: 2→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 14 307 4865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0214627
X-RAY DIFFRACTIONr_angle_refined_deg2.7251.9466242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6585602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14425.605223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70315729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3161515
X-RAY DIFFRACTIONr_chiral_restr0.2130.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023617
X-RAY DIFFRACTIONr_nbd_refined0.2320.22043
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2277
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.214
X-RAY DIFFRACTIONr_mcbond_it1.4071.53142
X-RAY DIFFRACTIONr_mcangle_it2.06224719
X-RAY DIFFRACTIONr_scbond_it3.59231718
X-RAY DIFFRACTIONr_scangle_it4.9754.51523
X-RAY DIFFRACTIONr_sphericity_free11.2314
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 252 -
Rwork0.327 2759 -
obs--100 %

+
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