[English] 日本語
Yorodumi
- PDB-3m5k: Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitrored... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m5k
TitleCrystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (BDI_1728) from Parabacteroides distasonis ATCC 8503 at 1.86 A resolution
ComponentsPutative NADH dehydrogenase/NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / Unknown ligand / Putative NADH dehydrogenase/NAD(P)H nitroreductase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.86 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (BDI_1728) from Parabacteroides distasonis ATCC 8503 at 1.86 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative NADH dehydrogenase/NAD(P)H nitroreductase
B: Putative NADH dehydrogenase/NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9127
Polymers39,9642
Non-polymers9485
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-48 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.639, 149.639, 149.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

21B-411-

HOH

31B-455-

HOH

Noncrystallographic symmetry (NCS)NCS domain: (Details: A) / NCS domain segments: (Refine code: 4 )
DetailsSTATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Putative NADH dehydrogenase/NAD(P)H nitroreductase


Mass: 19982.137 Da / Num. of mol.: 2 / Fragment: sequence database residues 24-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_1728 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LCR1
#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-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 24-194) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 24-194) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.47
Details: 14.0000% polyethylene glycol 1000, 0.3000M sodium chloride, 0.1M Na/K phosphate pH 6.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97946,0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979461
30.979321
ReflectionResolution: 1.86→29.347 Å / Num. obs: 48462 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.669 % / Biso Wilson estimate: 25.884 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.86-1.930.8212.153090944899.7
1.93-20.559347083825199.9
2-2.090.405451744903899.9
2.09-2.20.2745.852560914499.9
2.2-2.340.217.952131927899.7
2.34-2.520.15310.252388908999.9
2.52-2.780.1114.353743933899.9
2.78-3.180.07919.2516799024100
3.18-40.0532750394906999.9
4-29.3470.03832.951796913599.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.86→29.347 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.007 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.092
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. FLAVIN MONONUCLEOTIDE COFACTOR (FMN) AND AN UNKNOWN LIGAND (UNL) ARE MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH MONOMER. DURING THE REFINEMENT, THE FMN RESTRAINTS DICTIONARY WAS MODIFIED TO ALLOW BENDING OF THE ISOALLOXAZINE RING ALONG THE N5-N10 VIRTUAL AXIS RESULTING IN AN IMPROVED FIT BETWEEN THE FMN COORDINATES AND ELECTRON DENSITY. 4. CHLORIDE ION (CL) FROM CRYSTALLIZATION IS MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2446 5.1 %RANDOM
Rwork0.16 ---
obs0.161 48417 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.01 Å2 / Biso mean: 26.696 Å2 / Biso min: 10.66 Å2
Refinement stepCycle: LAST / Resolution: 1.86→29.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 79 366 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223152
X-RAY DIFFRACTIONr_bond_other_d0.0020.022188
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9934330
X-RAY DIFFRACTIONr_angle_other_deg0.98835344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79523.233133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84315578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5341530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023589
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
X-RAY DIFFRACTIONr_nbd_refined0.2240.2672
X-RAY DIFFRACTIONr_nbd_other0.2060.22402
X-RAY DIFFRACTIONr_nbtor_refined0.170.21539
X-RAY DIFFRACTIONr_nbtor_other0.0840.21565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.228
X-RAY DIFFRACTIONr_mcbond_it1.95132121
X-RAY DIFFRACTIONr_mcbond_other0.5633738
X-RAY DIFFRACTIONr_mcangle_it2.50743157
X-RAY DIFFRACTIONr_scbond_it3.38351395
X-RAY DIFFRACTIONr_scangle_it4.65361173
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeWeight position
11A2612X-RAY DIFFRACTIONMEDIUM POSITIONAL0.5
11A2612X-RAY DIFFRACTIONMEDIUM THERMAL2
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 180 -
Rwork0.247 3329 -
all-3509 -
obs--99.86 %

+
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