[English] 日本語
Yorodumi
- PDB-7l9q: Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-1) at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l9q
TitleWild-type Pseudomonas fluorescens isocyanide hydratase (WT-1) at 274K, Refmac5-refined
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / isocyanide / isonitrile / DJ-1/PfpI superfamily / diffuse scattering
Function / homology: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / regulation of DNA-templated transcription / Isonitrile hydratase InhA
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.149 Å
AuthorsSu, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / Wilson, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139978 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123159 United States
CitationJournal: Struct Dyn. / Year: 2021
Title: Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.
Authors: Su, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / Wilson, M.A.
History
DepositionJan 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isonitrile hydratase InhA
B: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)48,3612
Polymers48,3612
Non-polymers00
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-31 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.305, 58.188, 69.015
Angle α, β, γ (deg.)90.000, 112.808, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Isonitrile hydratase InhA


Mass: 24180.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria)
Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: inhA, PFL_4109 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977, EC: 4.2.1.103
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 23% PEG3350, 100 mM Tris-HCl, pH 8.6, 200 mM magnesium chloride, 2 mM DTT

-
Data collection

DiffractionMean temperature: 274 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2019
Details: FLAT SI RH COATED M0, KIRKPATRICK-BAEZ FLAT BENT SI M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 1.149→39.142 Å / Num. obs: 138486 / % possible obs: 93.5 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rrim(I) all: 0.058 / Net I/σ(I): 12.9
Reflection shellResolution: 1.149→1.17 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6553 / CC1/2: 0.483 / Rrim(I) all: 1.28 / % possible all: 89.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NI6

6ni6


Resolution: 1.149→39.142 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.12 / SU ML: 0.022 / Cross valid method: FREE R-VALUE / ESU R: 0.031 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.144 4137 2.988 %random
Rwork0.1209 134320 --
all0.122 ---
obs-138457 93.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.024 Å20 Å20.107 Å2
2---0.04 Å20 Å2
3----0.055 Å2
Refinement stepCycle: LAST / Resolution: 1.149→39.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 363 3731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134128
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173970
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.6395719
X-RAY DIFFRACTIONr_angle_other_deg1.4911.5729128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.62821.075214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88915627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8361537
X-RAY DIFFRACTIONr_chiral_restr0.0850.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025086
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02989
X-RAY DIFFRACTIONr_nbd_refined0.2270.2816
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23268
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21926
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0810.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.210
X-RAY DIFFRACTIONr_nbd_other0.2170.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.215
X-RAY DIFFRACTIONr_mcbond_it1.1761.452162
X-RAY DIFFRACTIONr_mcbond_other1.1681.4482161
X-RAY DIFFRACTIONr_mcangle_it1.5212.1842783
X-RAY DIFFRACTIONr_mcangle_other1.5232.1862784
X-RAY DIFFRACTIONr_scbond_it1.7741.8481966
X-RAY DIFFRACTIONr_scbond_other1.7741.8491967
X-RAY DIFFRACTIONr_scangle_it2.2562.6422936
X-RAY DIFFRACTIONr_scangle_other2.2562.6432937
X-RAY DIFFRACTIONr_lrange_it2.81118.6854498
X-RAY DIFFRACTIONr_lrange_other2.59218.2234439
X-RAY DIFFRACTIONr_rigid_bond_restr1.29638098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.149-1.1790.2482810.2499500X-RAY DIFFRACTION89.586
1.179-1.2120.2372710.2298971X-RAY DIFFRACTION86.5842
1.212-1.2470.2423050.2129479X-RAY DIFFRACTION94.6778
1.247-1.2850.1952850.1899294X-RAY DIFFRACTION94.6729
1.285-1.3270.1812830.1718953X-RAY DIFFRACTION94.573
1.327-1.3740.1682760.1478636X-RAY DIFFRACTION94.6876
1.374-1.4260.1472470.1218346X-RAY DIFFRACTION93.892
1.426-1.4840.1452340.117473X-RAY DIFFRACTION87.8391
1.484-1.550.1222660.0947544X-RAY DIFFRACTION92.6783
1.55-1.6250.1172310.0887521X-RAY DIFFRACTION96.5741
1.625-1.7130.1181710.0837257X-RAY DIFFRACTION96.6181
1.713-1.8170.1022050.0866786X-RAY DIFFRACTION96.0698
1.817-1.9420.1111880.0886295X-RAY DIFFRACTION95.1703
1.942-2.0980.1181630.0925492X-RAY DIFFRACTION89.0131
2.098-2.2980.1212110.15334X-RAY DIFFRACTION94.4473
2.298-2.5690.1171550.1055013X-RAY DIFFRACTION97.7677
2.569-2.9650.1831310.1244407X-RAY DIFFRACTION96.656
2.965-3.630.1451020.1253648X-RAY DIFFRACTION93.7734
3.63-5.1250.132630.1182711X-RAY DIFFRACTION89.3686
5.125-39.1420.171690.1581661X-RAY DIFFRACTION98.4633

+
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