[English] 日本語
Yorodumi
- PDB-4g8s: Crystal Structure Of a Putative Nitroreductase from Geobacter sul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g8s
TitleCrystal Structure Of a Putative Nitroreductase from Geobacter sulfurreducens PCA (Target PSI-013445)
ComponentsNitroreductase family protein
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium (NYSGRC)
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Nitroreductase-like family 3 protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKumar, P.R. / Bhosle, R. / Hillerich, B. / Seidel, R. / Toro, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a nitroreductase from Geobacter sulfurreducens PCA
Authors: Kumar, P.R. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Seidel, R. / Stead, M. / ...Authors: Kumar, P.R. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Seidel, R. / Stead, M. / Toro, R. / Washington, E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitroreductase family protein
B: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8565
Polymers46,8512
Non-polymers1,0053
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-32 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.759, 73.759, 169.472
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer

-
Components

#1: Protein Nitroreductase family protein


Mass: 23425.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA, ATCC 51573 / Gene: GSU0217 / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q74GM9
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (0.2M Potassium Chloride, 20% PEG 3350 - MCSG1 #89), Cryoprotection (Ethylene glycol), Sitting Drop, Vapor Diffusion, ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (0.2M Potassium Chloride, 20% PEG 3350 - MCSG1 #89), Cryoprotection (Ethylene glycol), Sitting Drop, Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 45382 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 35.58 Å2 / Rmerge(I) obs: 0.097 / Χ2: 2.21 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2412.70.79122671.3461100
2.24-2.2812.70.66222291.4491100
2.28-2.3212.70.59323191.4381100
2.32-2.3712.80.52522601.4481100
2.37-2.4212.70.44922731.4641100
2.42-2.4812.80.40522341.4821100
2.48-2.5412.80.32823201.5421100
2.54-2.6112.80.26522371.6231100
2.61-2.6912.80.24322571.7021100
2.69-2.7712.70.19222711.841100
2.77-2.8712.70.17322531.8981100
2.87-2.9912.60.1522962.0551100
2.99-3.1212.50.12322602.3581100
3.12-3.2912.30.10222702.6421100
3.29-3.4911.90.08422843.1541100
3.49-3.7611.40.07322483.51100
3.76-4.1411.10.06422843.7141100
4.14-4.7411.10.05422723.7591100
4.74-5.9711.50.05122703.4771100
5.97-5012.10.0422783.146199.3

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→36.738 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8825 / SU ML: 0.16 / σ(F): 0 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1971 1990 8.15 %RANDOM
Rwork0.1623 ---
obs0.1651 24421 99.4 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.78 Å2 / Biso mean: 31.9928 Å2 / Biso min: 10.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 68 109 2974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082939
X-RAY DIFFRACTIONf_angle_d1.0293993
X-RAY DIFFRACTIONf_chiral_restr0.066437
X-RAY DIFFRACTIONf_plane_restr0.005515
X-RAY DIFFRACTIONf_dihedral_angle_d13.4941088
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 (%)
2.2002-2.25520.22271340.19081545167998
2.2552-2.31620.24931390.17991555169498
2.3162-2.38430.20191400.17551561170199
2.3843-2.46130.23461390.16761566170599
2.4613-2.54920.20231390.1661553169299
2.5492-2.65130.22261400.160315781718100
2.6513-2.77190.19511400.163815811721100
2.7719-2.9180.21321430.170216011744100
2.918-3.10070.24821410.174815911732100
3.1007-3.340.20781420.178516111753100
3.34-3.67580.17791440.149916231767100
3.6758-4.20710.16981450.1416301775100
4.2071-5.29790.16281490.138616701819100
5.2979-36.74350.20481550.18491766192199
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)
11.76230.43010.22.42910.39351.1024-0.0466-0.09860.05030.18480.0770.2353-0.1085-0.0895-0.02340.29760.0027-0.03310.0565-0.00290.215723.14857.363665.8817
21.58090.11460.01861.6776-0.45580.1256-0.08820.1199-0.17710.1587-0.02360.1080.3485-0.035-0.02660.3269-0.0226-0.03810.0666-0.01430.173730.95996.569859.4582
30.669-0.25680.09881.5495-0.06560.467-0.01390.12470.063-0.2626-0.02290.3155-0.0298-0.0165-0.06350.3103-0.0307-0.04910.07280.03260.231118.31695.715858.3476
42.2562-0.19840.22531.90960.36452.1119-0.04890.3140.1741-0.1250.0371-0.2756-0.31160.526-0.06770.2528-0.0974-0.03640.228-0.00040.21945.94189.750654.3674
53.29210.2434-0.15781.67040.34191.7751-0.27280.331-0.0177-0.40890.33640.0243-0.04480.22130.06150.3304-0.0286-0.05420.11960.00460.131937.65976.054858.5949
63.10220.21530.00533.6406-0.10062.8593-0.06980.1191-0.1734-0.11370.0435-0.46470.17170.62240.05350.18240.0188-0.01270.2467-0.06420.208849.03222.18257.6976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:98)A1 - 98
2X-RAY DIFFRACTION2chain 'A' and (resseq 99:133)A99 - 133
3X-RAY DIFFRACTION3chain 'A' and (resseq 134:187)A134 - 187
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:98)B1 - 98
5X-RAY DIFFRACTION5chain 'B' and (resseq 99:133)B99 - 133
6X-RAY DIFFRACTION6chain 'B' and (resseq 134:186)B134 - 186

+
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