[English] 日本語
Yorodumi
- PDB-4dn2: CRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dn2
TitleCRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metallireducens GS-15
ComponentsNitroreductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
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 metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metallireducens GS-15
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitroreductase
B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3604
Polymers46,4482
Non-polymers9132
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-46 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.884, 64.161, 61.384
Angle α, β, γ (deg.)90.000, 98.140, 90.000
Int Tables number4
Space group name H-MP1211
Detailsdimer

-
Components

#1: Protein Nitroreductase /


Mass: 23223.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (bacteria) / Strain: GS-15 / Gene: ABB33053.1, Gmet_2835 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q39RS1
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M NaCl, 0.1M Na2HPO4:citric acid, pH 4.2, 20% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 2.3 % / Av σ(I) over netI: 22.04 / Number: 235062 / Rmerge(I) obs: 0.049 / Χ2: 1.27 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 104230 / % possible obs: 95.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.075095.910.032.252.4
3.234.0799.310.0312.082.3
2.823.2399.310.0452.32.3
2.562.8299.410.052.0232.3
2.382.5699.810.0541.622.3
2.242.3899.710.0651.492.3
2.132.2499.910.0751.3472.3
2.042.1399.810.0971.2262.3
1.962.0499.910.1191.1322.3
1.891.9699.810.161.0072.3
1.831.8999.910.2050.9572.3
1.781.8399.910.2780.862.3
1.731.7899.910.3510.8652.3
1.691.7399.810.4540.852.3
1.651.6999.910.5140.7972.3
1.621.6599.710.6720.7592.2
1.581.6297.410.7750.7812.1
1.551.5890.810.8510.7452
1.531.5578.310.8690.7611.9
1.51.5355.610.9380.7291.7
ReflectionResolution: 1.5→50 Å / Num. obs: 104230 / % possible obs: 95.7 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.049 / Χ2: 1.272 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.531.70.93829880.729155.6
1.53-1.551.90.86942830.761178.3
1.55-1.5820.85149190.745190.8
1.58-1.622.10.77553960.781197.4
1.62-1.652.20.67253900.759199.7
1.65-1.692.30.51454490.797199.9
1.69-1.732.30.45454280.85199.8
1.73-1.782.30.35154250.865199.9
1.78-1.832.30.27853970.86199.9
1.83-1.892.30.20554640.957199.9
1.89-1.962.30.1654331.007199.8
1.96-2.042.30.11955001.132199.9
2.04-2.132.30.09754361.226199.8
2.13-2.242.30.07553971.347199.9
2.24-2.382.30.06554391.49199.7
2.38-2.562.30.05454481.62199.8
2.56-2.822.30.0554042.023199.4
2.82-3.232.30.04554192.3199.3
3.23-4.072.30.03153882.08199.3
4.07-502.40.0352272.25195.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→19.97 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1923 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8578 / SU B: 3.728 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0897 / SU Rfree: 0.0751 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 2732 5.1 %RANDOM
Rwork0.1521 ---
obs0.1542 53864 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.09 Å2 / Biso mean: 27.8939 Å2 / Biso min: 14.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.24 Å2
2---0.07 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 62 186 3219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193125
X-RAY DIFFRACTIONr_angle_refined_deg1.2142.0134258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81223.869137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49215490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3411522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212398
X-RAY DIFFRACTIONr_rigid_bond_restr2.72333125
X-RAY DIFFRACTIONr_sphericity_free20.693587
X-RAY DIFFRACTIONr_sphericity_bonded12.33653148
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 163 -
Rwork0.324 2843 -
all-3006 -
obs--75.21 %
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)
10.37010.0509-0.05720.353-0.03150.80050.00680.0239-0.0071-0.0025-0.0281-0.00190.06640.04450.02130.0110.0049-0.00950.01330.00070.024925.214116.062565.6825
20.315-0.0125-0.00070.2246-0.05021.0240.0123-0.04910.01210.0528-0.02150.01460.04220.00840.00910.0212-0.0068-0.00620.0124-0.00470.024820.763317.426683.8657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

+
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