[English] 日本語
Yorodumi
- PDB-3dtt: Crystal structure of a putative f420 dependent nadp-reductase (ar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dtt
TitleCrystal structure of a putative f420 dependent nadp-reductase (arth_0613) from arthrobacter sp. fb24 at 1.70 A resolution
ComponentsNADP oxidoreductase
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP oxidoreductase, coenzyme F420-dependent
Similarity search - Component
Biological speciesArthrobacter sp. FB24 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative coenzyme F420H2:NADP+ oxidoreductase (YP_830112.1) from Arthrobacter sp. FB24 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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: NADP oxidoreductase
B: NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7477
Polymers52,1072
Non-polymers1,6405
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-41 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.974, 47.053, 61.125
Angle α, β, γ (deg.)77.430, 73.210, 64.330
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein NADP oxidoreductase / coenzyme F420-dependent precursor


Mass: 26053.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. FB24 (bacteria) / Gene: YP_830112.1, Arth_0613 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0JSJ2
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#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.: 547 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M ammonium acetate, 30.0% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97951,0.97966
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 26, 2008 / 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
10.911621
20.979511
30.979661
ReflectionResolution: 1.7→58.222 Å / Num. obs: 40912 / % possible obs: 95 % / Redundancy: 2 % / Biso Wilson estimate: 14.781 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.790.2652.51018251410.26581.9
1.79-1.90.1923.61137557280.19296.1
1.9-2.030.1324.61074454080.13296.3
2.03-2.190.0858.4996650180.08596.8
2.19-2.40.0739.6927746730.07397.3
2.4-2.690.06311.3835542060.06397.5
2.69-3.10.05113.7747237630.05198
3.1-3.80.03916.4628731680.03998.3
3.8-5.380.03717.2488624580.03798.6
5.38-58.220.03518.5267213490.03598.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→58.222 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.962 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.111
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. NADP (NAP) AND ACETATE (ACT) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2002 4.9 %RANDOM
Rwork0.16 ---
obs0.162 40802 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.554 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.64 Å2-0.14 Å2
2---1 Å2-0.14 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→58.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 105 547 3830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223401
X-RAY DIFFRACTIONr_bond_other_d0.0030.022139
X-RAY DIFFRACTIONr_angle_refined_deg1.56624673
X-RAY DIFFRACTIONr_angle_other_deg1.36535283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5695456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36324.435115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.61415497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9661516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023788
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02612
X-RAY DIFFRACTIONr_nbd_refined0.1720.2636
X-RAY DIFFRACTIONr_nbd_other0.1420.22252
X-RAY DIFFRACTIONr_nbtor_refined0.1450.21633
X-RAY DIFFRACTIONr_nbtor_other0.0730.21581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.070.2466
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.249
X-RAY DIFFRACTIONr_mcbond_it0.92322533
X-RAY DIFFRACTIONr_mcbond_other0.1432910
X-RAY DIFFRACTIONr_mcangle_it1.38143540
X-RAY DIFFRACTIONr_scbond_it2.561268
X-RAY DIFFRACTIONr_scangle_it3.38781124
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 100 -
Rwork0.221 2192 -
all-2292 -
obs--71.56 %
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)
10.6494-0.42670.07271.41780.18710.594-0.0998-0.0880.03230.27720.0929-0.06140.011-0.00080.0069-0.04450.0081-0.014-0.1165-0.0047-0.144827.47650.79614.203
20.51320.04990.06780.91980.29590.7050.01460.0665-0.0002-0.1860.01-0.0051-0.05710.0192-0.0246-0.0586-0.00640.0077-0.12180.0009-0.145327.54528.191-11.93
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 4019 - 59
2X-RAY DIFFRACTION1AA48 - 22667 - 245
3X-RAY DIFFRACTION2BB0 - 4219 - 61
4X-RAY DIFFRACTION2BB48 - 22667 - 245

+
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