[English] 日本語
Yorodumi
- PDB-1yde: Crystal Structure of Human Retinal Short-Chain Dehydrogenase/Redu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yde
TitleCrystal Structure of Human Retinal Short-Chain Dehydrogenase/Reductase 3
ComponentsRetinal dehydrogenase/reductase 3
KeywordsOXIDOREDUCTASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Estrogen biosynthesis / estradiol 17-beta-dehydrogenase [NAD(P)] activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / steroid catabolic process / identical protein binding / cytosol
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLukacik, P. / Bunkozci, G. / Kavanagh, K. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.J. / Year: 2007
Title: Structural and biochemical characterization of human orphan DHRS10 reveals a novel cytosolic enzyme with steroid dehydrogenase activity.
Authors: Lukacik, P. / Keller, B. / Bunkoczi, G. / Kavanagh, K.L. / Kavanagh, K. / Lee, W.H. / Hwa Lee, W. / Adamski, J. / Oppermann, U.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinal dehydrogenase/reductase 3
B: Retinal dehydrogenase/reductase 3
C: Retinal dehydrogenase/reductase 3
D: Retinal dehydrogenase/reductase 3
E: Retinal dehydrogenase/reductase 3
F: Retinal dehydrogenase/reductase 3
G: Retinal dehydrogenase/reductase 3
H: Retinal dehydrogenase/reductase 3
I: Retinal dehydrogenase/reductase 3
J: Retinal dehydrogenase/reductase 3
K: Retinal dehydrogenase/reductase 3
L: Retinal dehydrogenase/reductase 3
M: Retinal dehydrogenase/reductase 3
N: Retinal dehydrogenase/reductase 3
O: Retinal dehydrogenase/reductase 3
P: Retinal dehydrogenase/reductase 3


Theoretical massNumber of molelcules
Total (without water)453,27016
Polymers453,27016
Non-polymers00
Water22,5371251
1
A: Retinal dehydrogenase/reductase 3
B: Retinal dehydrogenase/reductase 3
C: Retinal dehydrogenase/reductase 3
D: Retinal dehydrogenase/reductase 3


Theoretical massNumber of molelcules
Total (without water)113,3184
Polymers113,3184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-104 kcal/mol
Surface area34930 Å2
MethodPISA
2
E: Retinal dehydrogenase/reductase 3
F: Retinal dehydrogenase/reductase 3
G: Retinal dehydrogenase/reductase 3
H: Retinal dehydrogenase/reductase 3


Theoretical massNumber of molelcules
Total (without water)113,3184
Polymers113,3184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13470 Å2
ΔGint-109 kcal/mol
Surface area35220 Å2
MethodPISA
3
I: Retinal dehydrogenase/reductase 3
J: Retinal dehydrogenase/reductase 3
K: Retinal dehydrogenase/reductase 3
L: Retinal dehydrogenase/reductase 3


Theoretical massNumber of molelcules
Total (without water)113,3184
Polymers113,3184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-107 kcal/mol
Surface area35220 Å2
MethodPISA
4
M: Retinal dehydrogenase/reductase 3
N: Retinal dehydrogenase/reductase 3
O: Retinal dehydrogenase/reductase 3
P: Retinal dehydrogenase/reductase 3


Theoretical massNumber of molelcules
Total (without water)113,3184
Polymers113,3184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-112 kcal/mol
Surface area35460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.115, 98.823, 167.463
Angle α, β, γ (deg.)90.00, 115.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
12D
22B
32F
42H
52J
62L
72N
82P

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYTYRAA4 - 2534 - 253
21GLYTYRCC4 - 2534 - 253
31GLYTYREE4 - 2534 - 253
41ARGGLYGG6 - 2526 - 252
51TYRTYRII7 - 2537 - 253
61GLYTYRKK4 - 2534 - 253
71LYSTYRMM10 - 25310 - 253
81TYRTYROO7 - 2537 - 253
12GLYSERDD4 - 2584 - 258
22THRALABB3 - 2573 - 257
32GLYARGFF4 - 2594 - 259
42THRSERHH5 - 2585 - 258
52GLYSERJJ4 - 2584 - 258
62GLYSERLL4 - 2584 - 258
72LYSALANN10 - 25710 - 257
82ARGARGPP6 - 2596 - 259

NCS ensembles :
ID
1
2
DetailsBiological subunit is a tetramer, of which there are 4 in the ASU.

-
Components

#1: Protein
Retinal dehydrogenase/reductase 3


Mass: 28329.393 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: retSDR3A-p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BPX1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1251 / 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: 2.5 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Magnesium Acetate, MPD, cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 176307 / Num. obs: 176307 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 1.8 / Num. unique all: 17963 / Rsym value: 0.706 / % possible all: 0.648

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 17.186 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22903 3559 2 %RANDOM
Rwork0.18067 ---
all0.18166 172629 --
obs0.18166 172629 91.88 %-
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: 5.147 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20.75 Å2
2---2.41 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29359 0 0 1251 30610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02229913
X-RAY DIFFRACTIONr_bond_other_d0.0020.0228244
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.97940683
X-RAY DIFFRACTIONr_angle_other_deg0.919365404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80853987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45924.0421153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.884154768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.415217
X-RAY DIFFRACTIONr_chiral_restr0.0880.24758
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0233868
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025709
X-RAY DIFFRACTIONr_nbd_refined0.2060.26483
X-RAY DIFFRACTIONr_nbd_other0.1860.228937
X-RAY DIFFRACTIONr_nbtor_refined0.1730.214990
X-RAY DIFFRACTIONr_nbtor_other0.0880.218046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.21312
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.2222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.413320396
X-RAY DIFFRACTIONr_mcbond_other0.34638294
X-RAY DIFFRACTIONr_mcangle_it2.116531575
X-RAY DIFFRACTIONr_scbond_it4.158810825
X-RAY DIFFRACTIONr_scangle_it5.927119107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1415tight positional0.060.05
12C1415tight positional0.060.05
13E1415tight positional0.060.05
14G1415tight positional0.060.05
15I1415tight positional0.050.05
16K1415tight positional0.050.05
17M1415tight positional0.030.05
18O1415tight positional0.030.05
21D1391tight positional0.050.05
22B1391tight positional0.050.05
23F1391tight positional0.040.05
24H1391tight positional0.050.05
25J1391tight positional0.050.05
26L1391tight positional0.040.05
27N1391tight positional0.030.05
28P1391tight positional0.030.05
11A2006medium positional0.480.5
12C2006medium positional0.390.5
13E2006medium positional0.450.5
14G2006medium positional0.40.5
15I2006medium positional0.420.5
16K2006medium positional0.440.5
17M2006medium positional0.470.5
18O2006medium positional0.440.5
21D1944medium positional0.340.5
22B1944medium positional0.430.5
23F1944medium positional0.50.5
24H1944medium positional0.450.5
25J1944medium positional0.420.5
26L1944medium positional0.460.5
27N1944medium positional0.460.5
28P1944medium positional0.450.5
11A1415tight thermal1.4910
12C1415tight thermal1.5910
13E1415tight thermal1.5210
14G1415tight thermal1.6710
15I1415tight thermal1.6910
16K1415tight thermal1.5110
17M1415tight thermal2.0110
18O1415tight thermal2.1810
21D1391tight thermal1.7210
22B1391tight thermal2.1910
23F1391tight thermal1.6110
24H1391tight thermal1.8310
25J1391tight thermal2.0310
26L1391tight thermal1.8510
27N1391tight thermal2.0410
28P1391tight thermal1.9110
11A2006medium thermal2.310
12C2006medium thermal2.3410
13E2006medium thermal2.4910
14G2006medium thermal2.210
15I2006medium thermal2.3110
16K2006medium thermal2.4110
17M2006medium thermal2.2810
18O2006medium thermal2.710
21D1944medium thermal2.4310
22B1944medium thermal2.6710
23F1944medium thermal2.3310
24H1944medium thermal2.210
25J1944medium thermal2.2910
26L1944medium thermal2.5310
27N1944medium thermal2.7210
28P1944medium thermal2.6510
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 113 -
Rwork0.265 5090 -
obs--37.09 %

+
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