[English] 日本語
Yorodumi
- PDB-1ycg: X-ray Structures of Moorella thermoacetica FprA. Novel Diiron Sit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ycg
TitleX-ray Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase
ComponentsNitric oxide reductase
KeywordsOXIDOREDUCTASE / Nitric oxide / reductase / diiron site
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity, acting on NAD(P)H / FMN binding / electron transfer activity / metal ion binding
Similarity search - Function
Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin ...Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MU-OXO-DIIRON / FLAVIN MONONUCLEOTIDE / Nitric oxide reductase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsSilaghi-Dumitrescu, R. / Kurtz, D.M. / Lanzilotta, W.N.
CitationJournal: Biochemistry / Year: 2005
Title: X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase.
Authors: Silaghi-Dumitrescu, R. / Kurtz Jr, D.M. / Ljungdahl, L.G. / Lanzilotta, W.N.
History
DepositionDec 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 21, 2016Group: Other
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitric oxide reductase
B: Nitric oxide reductase
C: Nitric oxide reductase
D: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,37930
Polymers176,8794
Non-polymers3,50026
Water2,378132
1
A: Nitric oxide reductase
B: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,25516
Polymers88,4402
Non-polymers1,81514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-130 kcal/mol
Surface area29120 Å2
MethodPISA
2
C: Nitric oxide reductase
D: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,12414
Polymers88,4402
Non-polymers1,68512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-142 kcal/mol
Surface area29140 Å2
MethodPISA
3
A: Nitric oxide reductase
B: Nitric oxide reductase
hetero molecules

A: Nitric oxide reductase
B: Nitric oxide reductase
hetero molecules

C: Nitric oxide reductase
D: Nitric oxide reductase
hetero molecules

C: Nitric oxide reductase
D: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,75860
Polymers353,7588
Non-polymers7,00052
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation4_565y+1/2,-x+3/2,z+1/41
crystal symmetry operation5_653-x+3/2,y+1/2,-z-5/41
Buried area35900 Å2
ΔGint-582 kcal/mol
Surface area106930 Å2
MethodPISA
4
A: Nitric oxide reductase
B: Nitric oxide reductase
hetero molecules

A: Nitric oxide reductase
B: Nitric oxide reductase
hetero molecules

C: Nitric oxide reductase
D: Nitric oxide reductase
hetero molecules

C: Nitric oxide reductase
D: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,75860
Polymers353,7588
Non-polymers7,00052
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation4_565y+1/2,-x+3/2,z+1/41
crystal symmetry operation5_653-x+3/2,y+1/2,-z-5/41
Buried area38310 Å2
ΔGint-1214 kcal/mol
Surface area106090 Å2
MethodPISA
5
A: Nitric oxide reductase
B: Nitric oxide reductase
hetero molecules

C: Nitric oxide reductase
D: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,37930
Polymers176,8794
Non-polymers3,50026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_653-x+3/2,y+1/2,-z-5/41
Buried area18770 Å2
ΔGint-597 kcal/mol
Surface area53420 Å2
MethodPISA
6
C: Nitric oxide reductase
hetero molecules

B: Nitric oxide reductase
hetero molecules

A: Nitric oxide reductase
D: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,37930
Polymers176,8794
Non-polymers3,50026
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation5_653-x+3/2,y+1/2,-z-5/41
crystal symmetry operation5_643-x+3/2,y-1/2,-z-5/41
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-564 kcal/mol
Surface area60410 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13940 Å2
ΔGint-290 kcal/mol
Surface area57480 Å2
MethodPISA
8
B: Nitric oxide reductase
hetero molecules

D: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,19015
Polymers88,4402
Non-polymers1,75013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_653-x+3/2,y+1/2,-z-5/41
Buried area5450 Å2
ΔGint-291 kcal/mol
Surface area30870 Å2
MethodPISA
9
A: Nitric oxide reductase
hetero molecules

C: Nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,19015
Polymers88,4402
Non-polymers1,75013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_653-x+3/2,y+1/2,-z-5/41
Buried area5340 Å2
ΔGint-253 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.680, 159.680, 278.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThere are two copies of the biological (functional) dimer in the asymmetric unit the first is monomers A & B, and the second is monomers C & D

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Nitric oxide reductase / Type A flavoprotein fprA / FMN- protein fprA / Flavoprotein A


Mass: 44219.773 Da / Num. of mol.: 4 / Fragment: Scavenging Nitric Oxide Reducatase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FDN7, Oxidoreductases

-
Non-polymers , 5 types, 158 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 5.01 Å3/Da / Density % sol: 75.46 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.5
Details: 10 % PEG 3000, 200 mM Zinc acetate, 100 mM cacodylate buffer pH 6.5, LIQUID DIFFUSION, temperature 25K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 2003
RadiationMonochromator: ALS Beamline 5.0.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 88949 / Num. obs: 88890 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.08
Reflection shellResolution: 2.8→2.98 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→49.71 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3137495.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4459 5 %RANDOM
Rwork0.227 ---
all0.227 88949 --
obs0.227 88890 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.5213 Å2 / ksol: 0.307672 e/Å3
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---2.05 Å20 Å2
3---3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12460 0 166 132 12758
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.32
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 694 4.8 %
Rwork0.333 13913 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FMN_FEO.PARAMFMN_FEO.TOP
X-RAY DIFFRACTION3EGL.PAREGL.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

+
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://pdbjlvh1.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