[English] 日本語
Yorodumi
- PDB-4u9j: Crystal structure of an H-NOX protein from S. oneidensis in the M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u9j
TitleCrystal structure of an H-NOX protein from S. oneidensis in the Mn(II) ligation state, Q154A/Q155A/K156A mutant
ComponentsNO-binding heme-dependent sensor protein
KeywordsSIGNALING PROTEIN / H-NOX. hemoprotein / gas sensor
Function / homology
Function and homology information


heme binding / metal ion binding
Similarity search - Function
H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MANGANESE PROTOPORPHYRIN IX / NO-binding heme-dependent sensor protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHerzik Jr., M.A. / Jonnalagadda, R. / Kuriyan, J. / Marletta, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association11PRE7370086 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural insights into the role of iron-histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins.
Authors: Herzik, M.A. / Jonnalagadda, R. / Kuriyan, J. / Marletta, M.A.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NO-binding heme-dependent sensor protein
B: NO-binding heme-dependent sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6997
Polymers42,3142
Non-polymers1,3855
Water2,972165
1
A: NO-binding heme-dependent sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8614
Polymers21,1571
Non-polymers7043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NO-binding heme-dependent sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8383
Polymers21,1571
Non-polymers6812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.801, 163.801, 102.082
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-315-

HOH

-
Components

#1: Protein NO-binding heme-dependent sensor protein


Mass: 21157.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2144 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): RP523(DE3) / References: UniProt: Q8EF49
#2: Chemical ChemComp-MNH / MANGANESE PROTOPORPHYRIN IX


Mass: 615.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32MnN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 4.56 Å3/Da / Density % sol: 73.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: Obtained by equilibrating a 2 uL drop of 1:1 protein:reservoir against a 700 uL reservoir containing 1.6-1.9 M DL-malic acid (pH 7.3). For cryoprotection, 2 uL of mother liquor containing ...Details: Obtained by equilibrating a 2 uL drop of 1:1 protein:reservoir against a 700 uL reservoir containing 1.6-1.9 M DL-malic acid (pH 7.3). For cryoprotection, 2 uL of mother liquor containing 10% glycerol was added directly to the drop and crystals were serial transferred into mother liquor solution containing 5, 7.5 and 10% glycerol prior to flash freezing in liquid nitrogen. Crystal growth and manipulation was performed anaerobically.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.027 Å / Num. all: 86341 / Num. obs: 86341 / % possible obs: 96.52 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 1.1 / % possible all: 98.6

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U99

4u99


Resolution: 2.1→48.027 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 4389 5.08 %
Rwork0.171 --
obs0.1723 86341 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→48.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 89 165 3205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213157
X-RAY DIFFRACTIONf_angle_d1.654290
X-RAY DIFFRACTIONf_dihedral_angle_d14.5951152
X-RAY DIFFRACTIONf_chiral_restr0.344462
X-RAY DIFFRACTIONf_plane_restr0.011566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.35391420.35782421X-RAY DIFFRACTION86
2.1239-2.14890.35561210.33062513X-RAY DIFFRACTION88
2.1489-2.17510.31961200.32912534X-RAY DIFFRACTION89
2.1751-2.20260.36851220.30882608X-RAY DIFFRACTION92
2.2026-2.23160.37121550.29952619X-RAY DIFFRACTION93
2.2316-2.26220.28411570.2772674X-RAY DIFFRACTION95
2.2622-2.29450.2951550.27992725X-RAY DIFFRACTION97
2.2945-2.32870.26731530.25122737X-RAY DIFFRACTION97
2.3287-2.36510.27091430.24912796X-RAY DIFFRACTION99
2.3651-2.40390.26731520.22542827X-RAY DIFFRACTION99
2.4039-2.44530.29361400.2172828X-RAY DIFFRACTION99
2.4453-2.48980.24051350.222771X-RAY DIFFRACTION99
2.4898-2.53770.2421730.2132826X-RAY DIFFRACTION100
2.5377-2.58950.22411450.20262807X-RAY DIFFRACTION99
2.5895-2.64580.24171770.2032774X-RAY DIFFRACTION99
2.6458-2.70730.25321530.20482760X-RAY DIFFRACTION99
2.7073-2.7750.22251460.20222797X-RAY DIFFRACTION99
2.775-2.85010.21641300.19532809X-RAY DIFFRACTION99
2.8501-2.93390.21591500.19312809X-RAY DIFFRACTION99
2.9339-3.02860.23421500.18082794X-RAY DIFFRACTION99
3.0286-3.13680.21521700.18212746X-RAY DIFFRACTION99
3.1368-3.26240.19211430.17792786X-RAY DIFFRACTION98
3.2624-3.41080.15921490.16972779X-RAY DIFFRACTION98
3.4108-3.59060.19221570.15052763X-RAY DIFFRACTION98
3.5906-3.81550.17341270.15152773X-RAY DIFFRACTION97
3.8155-4.10990.15221690.13182733X-RAY DIFFRACTION97
4.1099-4.52320.14051540.1122725X-RAY DIFFRACTION97
4.5232-5.17710.16221410.11962748X-RAY DIFFRACTION97
5.1771-6.520.14391190.14462756X-RAY DIFFRACTION96
6.52-48.03930.16561410.14252714X-RAY DIFFRACTION95
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)
13.3132-0.44660.06221.9938-0.67761.51710.06680.6778-0.1224-0.855-0.0143-0.5156-0.21070.3063-0.3370.717-0.06090.11860.5724-0.16510.6282107.17313.9509-9.1137
21.457-1.4146-1.47613.52540.37692.08350.01180.00110.4499-0.28950.1294-0.3348-1.07890.3049-0.55380.7644-0.09120.00610.4708-0.07560.5086102.00627.2022-5.6592
31.80530.7634-0.05931.72920.97953.193-0.00070.1621-0.327-0.11680.0441-0.07590.0496-0.0159-0.0480.40860.0096-0.05240.2992-0.09340.458596.453812.14539.5463
46.89550.6697-0.22820.3616-0.43960.97490.10110.12930.0436-0.04880.0335-0.0077-0.2518-0.03410.02960.5550.0601-0.03960.3758-0.09650.476691.132322.856814.762
52.58023.2795-1.47875.65390.26225.0725-0.27570.1249-0.812-0.55990.4301-0.38860.05710.342-0.19750.4740.0311-0.06910.3257-0.10640.5044101.453411.65646.592
63.09080.98020.4883.61590.97784.1404-0.04180.0582-0.1344-0.56330.102-0.4054-0.04290.2979-0.23570.4364-0.04490.04920.336-0.08440.4542116.390842.314615.0172
75.22991.7185-1.17093.3991-1.5610.9515-0.25821.11570.9956-1.31120.2832-0.6794-1.00660.4947-1.04151.409-0.275-0.00740.80470.00770.7332111.806651.4148-6.4803
83.8271.46720.8912.98860.19813.1288-0.23730.47360.4912-0.85760.14630.4105-0.7724-0.0786-0.64730.9463-0.0402-0.08110.4365-0.0320.4947101.967744.09170.3673
90.29271.104-1.11444.3459-4.22114.226-0.6917-0.48420.04240.1850.1564-1.0438-0.25241.1190.49061.0482-0.06210.01250.9997-0.12861.145999.286464.8169-5.6845
102.23280.16870.81046.9295-1.58043.1698-0.230.7161-0.0857-1.25120.3808-0.2406-0.53140.3795-0.25670.9446-0.1170.01680.4957-0.08090.4218110.343742.16171.1243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:49
2X-RAY DIFFRACTION2chain A and resid 50:67
3X-RAY DIFFRACTION3chain A and resid 68:157
4X-RAY DIFFRACTION4chain A and resid 158:187
5X-RAY DIFFRACTION5chain A and resid 201
6X-RAY DIFFRACTION6chain B and resid 1:78
7X-RAY DIFFRACTION7chain B and resid 79:95
8X-RAY DIFFRACTION8chain B and resid 96:177
9X-RAY DIFFRACTION9chain B and resid 178:186
10X-RAY DIFFRACTION10chain B and resid 201

+
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