[English] 日本語
Yorodumi
- PDB-2o4c: Crystal Structure of D-Erythronate-4-phosphate Dehydrogenase Comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o4c
TitleCrystal Structure of D-Erythronate-4-phosphate Dehydrogenase Complexed with NAD
ComponentsErythronate-4-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Erythronate-4-phsphate / dehydrogenase / NAD / Tartrate / phosphate ion
Function / homology
Function and homology information


4-phosphoerythronate dehydrogenase / 4-phosphoerythronate dehydrogenase activity / 'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxine biosynthetic process / NAD binding / protein dimerization activity / cytosol
Similarity search - Function
Erythronate-4-phosphate dehydrogenase, dimerisation domain / Erythronate-4-phosphate dehydrogenase / Erythronate-4-phosphate dehydrogenase, dimerisation domain / PdxB, dimerisation domain superfamily / Domain of unknown function (DUF3410) / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain ...Erythronate-4-phosphate dehydrogenase, dimerisation domain / Erythronate-4-phosphate dehydrogenase / Erythronate-4-phosphate dehydrogenase, dimerisation domain / PdxB, dimerisation domain superfamily / Domain of unknown function (DUF3410) / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / Ribosomal Protein S8; Chain: A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / L(+)-TARTARIC ACID / Erythronate-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsHa, J.Y. / Lee, J.H. / Kim, K.H. / Kim, D.J. / Lee, H.H. / Kim, H.K. / Yoon, H.J. / Suh, S.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of d-Erythronate-4-phosphate Dehydrogenase Complexed with NAD
Authors: Ha, J.Y. / Lee, J.H. / Kim, K.H. / Kim, D.J. / Lee, H.H. / Kim, H.K. / Yoon, H.J. / Suh, S.W.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Erythronate-4-phosphate dehydrogenase
B: Erythronate-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7637
Polymers82,0992
Non-polymers1,6645
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-28 kcal/mol
Surface area31160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.914, 101.630, 142.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Erythronate-4-phosphate dehydrogenase


Mass: 41049.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1375, pdxb / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: Q9I3W9, 4-phosphoerythronate dehydrogenase

-
Non-polymers , 5 types, 172 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.25 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.7M ammonium dihydrogen phosphate, 0.4M ammonium tartrate, 0.1M sodium citrate (pH 5.6), 10mM cupric chloride, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A10.97930, 0.97946, 0.95000
SYNCHROTRONPhoton Factory AR-NW12A21
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDJun 25, 2004mirrors
ADSC QUANTUM 2102CCDJun 25, 2004mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double crystal monochromatorMADMx-ray1
2Si(111) double crystal monochromatorSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.979461
30.951
411
Reflection

D res high: 2.35 Å / D res low: 30 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
114.33449630.0530.845183599.8
214.43453470.0581.055176399.8
3143400920.0560.915168399.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.063099.710.0321.119
4.025.0699.910.0360.958
3.514.0210010.0430.997
3.193.5199.910.0540.876
2.963.1999.910.0790.785
2.792.9699.910.1130.738
2.652.7999.910.1640.721
2.532.6599.610.2280.704
2.432.5399.710.310.695
2.352.4399.310.3790.696
5.063099.720.042.099
4.025.0699.920.041.332
3.514.0210020.0461.163
3.193.5199.920.0560.964
2.963.1999.920.0820.875
2.792.9699.920.1160.816
2.652.7999.920.1640.764
2.532.6599.620.2240.727
2.432.5399.820.3050.717
2.352.4399.320.3750.714
5.063099.730.0341.354
4.025.0699.930.0381.092
3.514.0210030.0461.073
3.193.5199.930.0580.942
2.963.1999.830.0840.822
2.792.9699.930.1220.779
2.652.7999.730.1720.742
2.532.6599.830.2380.712
2.432.5399.330.3250.708
2.352.4399.230.3970.693
ReflectionResolution: 2.2→30 Å / Num. obs: 63477 / % possible obs: 99.9 % / Rmerge(I) obs: 0.049 / Χ2: 0.79 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.442 / Num. unique all: 6245 / Χ2: 0.746 / % possible all: 100

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.42 Å / D res low: 50 Å / FOM : 0.47 / Reflection: 45888
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97931.83-4.95
13 wavelength20.97950.98-5.64
13 wavelength30.951.33-3.39
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se38.980.0380.2470.2312.977
2Se40.3590.2870.2070.1392.701
3Se600.5820.3350.1653.296
4Se600.8490.1650.1282.904
Phasing MAD shell
Resolution (Å)FOM Reflection
8.75-500.782296
5.51-8.750.833949
4.3-5.510.794990
3.65-4.30.685823
3.22-3.650.536529
2.91-3.220.377091
2.68-2.910.237418
2.5-2.680.137792
Phasing dmFOM : 0.49 / FOM acentric: 0.49 / FOM centric: 0.58 / Reflection: 59175 / Reflection acentric: 54342 / Reflection centric: 4833
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-35.6440.940.960.8928712233638
3.9-6.30.930.930.87847274431029
3.1-3.90.80.810.74104019472929
2.8-3.10.540.540.48102559513742
2.4-2.80.240.240.251719116209982
2.2-2.40.080.080.0999859472513

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.77 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.335 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 5563 10 %RANDOM
Rwork0.225 ---
obs0.229 55468 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.484 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 109 167 6048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225996
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9928181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2295758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97522.09268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7215914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4371578
X-RAY DIFFRACTIONr_chiral_restr0.070.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024610
X-RAY DIFFRACTIONr_nbd_refined0.190.22742
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24032
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2322
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.212
X-RAY DIFFRACTIONr_mcbond_it0.5891.53863
X-RAY DIFFRACTIONr_mcangle_it0.9926000
X-RAY DIFFRACTIONr_scbond_it1.28332418
X-RAY DIFFRACTIONr_scangle_it2.0734.52181
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 374 -
Rwork0.291 3627 -
obs-4001 99.98 %

+
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://pdbjlvh1.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