[English] 日本語
Yorodumi
- PDB-3asv: The Closed form of serine dehydrogenase complexed with NADP+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3asv
TitleThe Closed form of serine dehydrogenase complexed with NADP+
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SDR family / Rossmann fold / short-chain dehydrogenase/reductase / L-allo-threonine dehydrogenase
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsYamazawa, R. / Nakajima, Y. / Yoshimoto, T. / Ito, K.
CitationJournal: J.Biochem. / Year: 2011
Title: Crystal structure of serine dehydrogenase from Escherichia coli: important role of the C-terminal region for closed-complex formation.
Authors: Yamazawa, R. / Nakajima, Y. / Mushiake, K. / Yoshimoto, T. / Ito, K.
History
DepositionDec 21, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
E: Short-chain dehydrogenase/reductase SDR
F: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,69818
Polymers163,6676
Non-polymers5,03012
Water6,251347
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,46512
Polymers109,1124
Non-polymers3,3548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area17800 Å2
ΔGint-100 kcal/mol
Surface area32050 Å2
MethodPISA
2
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
E: Short-chain dehydrogenase/reductase SDR
F: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,46512
Polymers109,1124
Non-polymers3,3548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17720 Å2
ΔGint-96 kcal/mol
Surface area32170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.859, 113.859, 197.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 27277.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL1-Blue / Gene: EcDH1_2106, YdfG / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN (ESCHERICHIA COLI XL1-BLUE) DOES NOT CURRENTLY EXIST IN UNIPROT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 % / Mosaicity: 0.906 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Na/K phosphate, lithium sulfate, Na acetate buffer, pH 4.5, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2009
RadiationMonochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 39711 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.126 / Χ2: 1.154 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.7540.32119910.3781100
2.75-2.840.29919700.3911100
2.8-2.8540.27420160.4291100
2.85-2.9140.24419480.4551100
2.91-2.9740.23419770.5051100
2.97-3.0440.20820020.5561100
3.04-3.1240.1919550.586199.9
3.12-3.240.19619980.655199.9
3.2-3.340.16919690.755199.8
3.3-3.440.16620190.8811100
3.4-3.5240.14219601.1981100
3.52-3.6640.13519921.493199.9
3.66-3.8340.12819871.6561100
3.83-4.0340.12219921.8241100
4.03-4.2940.11319992.107199.9
4.29-4.6240.10919822.393199.9
4.62-5.0840.09619992.0661100
5.08-5.8140.09620041.5221100
5.81-7.3240.08419901.3591100
7.32-503.80.05419611.91195.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ASU

3asu


Resolution: 2.7→20 Å / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 3235134 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood target using amplitudes
Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1991 5 %RANDOM
Rwork0.192 ---
obs-39634 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1537 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 74.06 Å2 / Biso mean: 34.253 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20 Å2
2--3.18 Å20 Å2
3----6.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11380 0 318 347 12045
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.42.5
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 208 -
Rwork0.264 --
obs-3949 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4nap.paramCNS_LOCAL:nap.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://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