[English] 日本語
Yorodumi
- PDB-3tm9: Y29A mutant of Vitreoscilla stercoraria hemoglobin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tm9
TitleY29A mutant of Vitreoscilla stercoraria hemoglobin
ComponentsBacterial hemoglobin
KeywordsOXYGEN TRANSPORT / globin 8-helix fold / oxygen storage
Function / homology
Function and homology information


cellular response to nitrosative stress / nitric oxide dioxygenase NAD(P)H activity / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bacterial hemoglobin
Similarity search - Component
Biological speciesVitreoscilla stercoraria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsRatakonda, S. / Anand, A. / Dikshit, K. / Stark, B.C. / Howard, A.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallographic structure determination of B10 mutants of Vitreoscilla hemoglobin: role of Tyr29 (B10) in the structure of the ligand-binding site.
Authors: Ratakonda, S. / Anand, A. / Dikshit, K. / Stark, B.C. / Howard, A.J.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Feb 28, 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: Bacterial hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,05914
Polymers15,6981
Non-polymers1,36113
Water2,054114
1
A: Bacterial hemoglobin
hetero molecules

A: Bacterial hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,11928
Polymers31,3962
Non-polymers2,72326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5950 Å2
ΔGint-64 kcal/mol
Surface area14650 Å2
Unit cell
Length a, b, c (Å)85.194, 46.426, 62.873
Angle α, β, γ (deg.)90.000, 128.840, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Bacterial hemoglobin / Soluble cytochrome O


Mass: 15698.171 Da / Num. of mol.: 1 / Mutation: Y29A
Source method: isolated from a genetically manipulated source
Details: Tyr29Ala mutant gene was cloned into the SmaI site of pBluescript 11KS+ under control of the native vgb gene promoter.
Source: (gene. exp.) Vitreoscilla stercoraria (bacteria) / Gene: vhb / Plasmid: PDH88 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P04252
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 27 mg/mL protein in 1.3M (NH4)2SO4, 0.05M NaH2P2O7, 3% ethylene glycol. Not streak-seeded, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 12, 2009
Details: Si(111) monochromator with sagittally bent second crystal
RadiationMonochromator: Si111 - sagittal second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→32.5 Å / Num. obs: 20497 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 41.13 Å2 / Rmerge(I) obs: 0.0707 / Rsym value: 0.0707 / Net I/σ(I): 11.002
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.8-1.8641.670.45371.690.4537147.8
1.864-1.9392.190.37942.090.3794161.9
3.878-32.53.580.031229.440.0312198

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PHASERphasing
REFMAC5.5.0109refinement
X-GENdata reduction
X-GENdata scaling
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→31.123 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 1984 9.76 %
Rwork0.1723 18349 -
obs0.1756 20333 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.3 Å2 / Biso mean: 25.1251 Å2 / Biso min: 9.37 Å2
Refinement stepCycle: LAST / Resolution: 1.72→31.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 91 114 1308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181270
X-RAY DIFFRACTIONf_angle_d1.4811719
X-RAY DIFFRACTIONf_chiral_restr0.056197
X-RAY DIFFRACTIONf_plane_restr0.009212
X-RAY DIFFRACTIONf_dihedral_angle_d16.956469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7198-1.76280.32491430.25421260140397
1.7628-1.81050.28311350.23561322145798
1.8105-1.86380.24861380.23411279141798
1.8638-1.92390.26191380.20361262140099
1.9239-1.99270.2011480.19171304145299
1.9927-2.07240.21941350.1751298143399
2.0724-2.16670.21131440.161413321476100
2.1667-2.28090.17671420.145713001442100
2.2809-2.42380.17121410.143113191460100
2.4238-2.61080.18311370.148513251462100
2.6108-2.87340.1831490.149513181467100
2.8734-3.28880.20871440.172513281472100
3.2888-4.1420.18791390.163113301469100
4.142-31.12780.21371510.182613721523100
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)
10.0543-0.08990.0030.2546-0.16080.19810.0079-0.0838-0.0543-0.0269-0.1534-0.02890.14710.0728-0.05590.13710.00050.0210.1879-0.00680.1341-7.5154-28.383712.7403
20.2129-0.10890.15250.2187-0.03370.1151-0.0846-0.2026-0.08360.16290.21790.0136-0.2163-0.55110.01810.15990.06170.00750.17350.00220.1091-24.1881-15.266812.3319
30.0431-0.04530.00420.03940.0060.0199-0.0356-0.2038-0.09210.00480.22810.084-0.1046-0.05990.00190.18240.02450.02260.144-0.01360.199-25.5589-6.1714.2055
40.0129-0.0024-0.00970.0011-0.01040.02160.1152-0.14410.1142-0.3128-0.0590.36340.0154-0.1694-0.00050.20070.0452-0.090.20530.00720.2638-31.5663-15.9133.3862
50.02870.0207-0.02280.0195-0.00450.010.0885-0.1098-0.0913-0.16340.0030.0163-0.03980.0060.00020.13170.00360.02210.13390.00790.1294-14.9758-24.94614.8935
60.32340.2051-0.20890.5791-0.0480.3835-0.21320.2804-0.1323-0.17530.4414-0.1935-0.1384-0.30630.11350.10430.1367-0.02240.03830.10530.1606-13.019-19.4831-5.4278
70.2068-0.0477-0.04820.13860.05910.2325-0.0614-0.24470.08420.063-0.0051-0.1625-0.2578-0.242-0.00990.16160.0327-0.0050.09680.00940.1018-15.28-15.36113.9878
80.1599-0.0982-0.03310.12560.06370.05430.0324-0.02340.0113-0.0015-0.1332-0.0922-0.1860.2351-0.00980.1231-0.00780.00170.13270.03740.1465-8.0095-14.4531.6259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 36)A0
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 43)A0
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 56)A0
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 67)A0
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 90)A0
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 115)A0
8X-RAY DIFFRACTION8chain 'A' and (resid 116 through 146)A0

+
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