[English] 日本語
Yorodumi
- PDB-1tu9: Crystal Structure of a Protein PA3967, a Structurally Highly Homo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tu9
TitleCrystal Structure of a Protein PA3967, a Structurally Highly Homologous to a Human Hemoglobin, from Pseudomonas aeruginosa PAO1
Componentshypothetical protein PA3967Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Heme / hemoglobin / Pseudomonas aeruginosa PAO1 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PROPANOIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsKim, Y. / Joachimiak, A. / Skarina, T. / Egorova, O. / Bochkarev, A. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of PA3967 from Pseudomonas aeruginosa PAO1, a Hypothetical Protein which is highly homologous to human Hemoglobin in structure.
Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Egorova, O. / Bochkarev, A. / Savchenko, A. / Edwards, A.
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein PA3967
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8805
Polymers15,0651
Non-polymers8154
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.557, 52.557, 182.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21A-349-

HOH

31A-361-

HOH

41A-521-

HOH

51A-527-

HOH

-
Components

#1: Protein hypothetical protein PA3967 / Hypothesis


Mass: 15065.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9HX49
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG3350, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9794
SYNCHROTRONAPS 19-ID21.74031, 1.74127, 1.6270
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 14, 2004mirrors
SBC-22CCDJun 14, 2004mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
21.740311
31.741271
41.6271
ReflectionResolution: 1.2→45.64 Å / Num. all: 47042 / Num. obs: 45270 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.2
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.7 / % possible all: 75.6

-
Processing

Software
NameVersionClassification
REFMAC5.2refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
CCP4phasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→45.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.248 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19057 4538 10 %RANDOM
Rwork0.16118 ---
all0.164 40732 --
obs0.164 40732 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.409 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.045 Å0.046 Å
Refinement stepCycle: LAST / Resolution: 1.2→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 56 272 1358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211160
X-RAY DIFFRACTIONr_bond_other_d0.0030.021030
X-RAY DIFFRACTIONr_angle_refined_deg1.4812.0621579
X-RAY DIFFRACTIONr_angle_other_deg1.13232365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8455142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.35321.73152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62415188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0771513
X-RAY DIFFRACTIONr_chiral_restr0.1850.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021328
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02259
X-RAY DIFFRACTIONr_nbd_refined0.4060.2333
X-RAY DIFFRACTIONr_nbd_other0.2820.21308
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1130.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4531.5886
X-RAY DIFFRACTIONr_mcbond_other0.4221.5282
X-RAY DIFFRACTIONr_mcangle_it1.55821090
X-RAY DIFFRACTIONr_scbond_it2.6773573
X-RAY DIFFRACTIONr_scangle_it3.7364.5487
X-RAY DIFFRACTIONr_rigid_bond_restr2.03532678
X-RAY DIFFRACTIONr_sphericity_free3.2893272
X-RAY DIFFRACTIONr_sphericity_bonded1.93432160
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.364 276
Rwork0.298 2225
obs-2225

+
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