[English] 日本語
Yorodumi
- PDB-4d3v: Structure of Bacillus subtilis Nitric Oxide Synthase I218V in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d3v
TitleStructure of Bacillus subtilis Nitric Oxide Synthase I218V in complex with N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]phenyl}thiophene-2-carboximidamide
ComponentsNITRIC OXIDE SYNTHASE OXYGENASE
KeywordsOXIDOREDUCTASE / INHIBITOR
Function / homology
Function and homology information


nitric-oxide synthase (flavodoxin) / nitric-oxide synthase activity / nitric oxide biosynthetic process / heme binding / metal ion binding
Similarity search - Function
Nitric oxide synthase, oxygenase subunit / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily ...Nitric oxide synthase, oxygenase subunit / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / N-PROPANOL / Chem-RFQ / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHolden, J.K. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors.
Authors: Holden, J.K. / Kang, S. / Hollingsworth, S.A. / Li, H. / Lim, N. / Chen, S. / Huang, H. / Xue, F. / Tang, W. / Silverman, R.B. / Poulos, T.L.
History
DepositionOct 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,62510
Polymers42,0551
Non-polymers1,5709
Water4,900272
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,25120
Polymers84,1112
Non-polymers3,14018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8610 Å2
ΔGint-69.6 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.550, 94.943, 62.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2248-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein NITRIC OXIDE SYNTHASE OXYGENASE / NOSOXY-LIKE PROTEIN


Mass: 42055.336 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34453, EC: 1.14.13.165

-
Non-polymers , 6 types, 281 molecules

#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-RFQ / N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]phenyl}thiophene-2-carboximidamide


Mass: 461.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21N4O2S2
#5: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


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

-
Details

Sequence detailsE25A, E26A, E316A AND I218V INTRODUCED. N TERMINAL RESIDUES GSH ARE CARRYOVER FROM THE CLEAVED HIS TAG.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.45 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 60 MM BIS-TRIS METHANE, 40 MM CITRIC ACID, 20% PEG3350, 1.9% 1-PROPANOL, PH 7.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999746
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999746 Å / Relative weight: 1
ReflectionResolution: 1.88→49.2 Å / Num. obs: 39483 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 30.05 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.5 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LWA

4lwa


Resolution: 1.88→49.198 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 2002 5.1 %
Rwork0.1724 --
obs0.1743 39297 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→49.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 106 272 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073125
X-RAY DIFFRACTIONf_angle_d1.3014239
X-RAY DIFFRACTIONf_dihedral_angle_d13.8851157
X-RAY DIFFRACTIONf_chiral_restr0.071435
X-RAY DIFFRACTIONf_plane_restr0.004543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9270.35431480.31942575X-RAY DIFFRACTION99
1.927-1.97910.30321440.27112608X-RAY DIFFRACTION99
1.9791-2.03740.28721360.25262621X-RAY DIFFRACTION99
2.0374-2.10310.28741340.23222642X-RAY DIFFRACTION99
2.1031-2.17830.2261220.20612661X-RAY DIFFRACTION100
2.1783-2.26550.24591500.1972607X-RAY DIFFRACTION99
2.2655-2.36860.22351600.16972641X-RAY DIFFRACTION100
2.3686-2.49350.21311660.16932614X-RAY DIFFRACTION99
2.4935-2.64970.20381410.16512650X-RAY DIFFRACTION99
2.6497-2.85430.24111240.17412672X-RAY DIFFRACTION100
2.8543-3.14150.21891300.17252696X-RAY DIFFRACTION100
3.1415-3.59590.19211390.1682702X-RAY DIFFRACTION100
3.5959-4.530.1681460.13662743X-RAY DIFFRACTION100
4.53-49.21440.18351620.15622863X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.4888 Å / Origin y: 19.4941 Å / Origin z: 22.6268 Å
111213212223313233
T0.2543 Å2-0.0179 Å20.0255 Å2-0.2251 Å2-0.0226 Å2--0.3295 Å2
L1.1778 °2-0.0008 °20.2226 °2-1.6412 °2-0.4225 °2--1.0842 °2
S-0.0418 Å °0.1676 Å °0.1457 Å °-0.1648 Å °0.057 Å °-0.1009 Å °-0.1362 Å °0.125 Å °-0.0072 Å °
Refinement TLS groupSelection details: ALL

+
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