[English] 日本語
Yorodumi
- PDB-1xu7: Crystal Structure of the Interface Open Conformation of Tetrameri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xu7
TitleCrystal Structure of the Interface Open Conformation of Tetrameric 11b-HSD1
ComponentsCorticosteroid 11-beta-dehydrogenase, isozyme 1
KeywordsOXIDOREDUCTASE / 11b-HSD1 / SDR / dehydrogenase / hydroxysteroid
Function / homology
Function and homology information


11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development / NADP binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / membrane
Similarity search - Function
short chain dehydrogenase / 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
Chem-NDP / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHosfield, D.J. / Wu, Y. / Skene, R.J. / Hilger, M. / Jennings, A. / Snell, G.P. / Aertgeerts, K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Conformational Flexibility in Crystal Structures of Human 11beta-hydroxysteroid dehydrogenase type I provide insights into glucocorticoid interconversion and enzyme regulation.
Authors: Hosfield, D.J. / Wu, Y. / Skene, R.J. / Hilger, M. / Jennings, A. / Snell, G.P. / Aertgeerts, K.
History
DepositionOct 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: 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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Corticosteroid 11-beta-dehydrogenase, isozyme 1
B: Corticosteroid 11-beta-dehydrogenase, isozyme 1
C: Corticosteroid 11-beta-dehydrogenase, isozyme 1
D: Corticosteroid 11-beta-dehydrogenase, isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,01814
Polymers127,3484
Non-polymers6,67110
Water8,755486
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Corticosteroid 11-beta-dehydrogenase, isozyme 1
D: Corticosteroid 11-beta-dehydrogenase, isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0097
Polymers63,6742
Non-polymers3,3355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-63 kcal/mol
Surface area20330 Å2
MethodPISA, PQS
3
A: Corticosteroid 11-beta-dehydrogenase, isozyme 1
B: Corticosteroid 11-beta-dehydrogenase, isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0097
Polymers63,6742
Non-polymers3,3355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-61 kcal/mol
Surface area20710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.430, 159.625, 73.544
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological tetramer

-
Components

#1: Protein
Corticosteroid 11-beta-dehydrogenase, isozyme 1 / 11-DH / 11-beta-hydroxysteroid dehydrogenase 1 / 11-beta-HSD1


Mass: 31836.875 Da / Num. of mol.: 4 / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L / Plasmid: pBAD-ThioE / Cell (production host): DH10b-Tir / Production host: Escherichia coli (E. coli)
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG , MES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.3404, 1.3408, 1.3412, 1.2782
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.34041
21.34081
31.34121
41.27821
ReflectionResolution: 1.8→20 Å / Num. all: 114558 / Num. obs: 114558 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.046 / Net I/σ(I): 26.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 9105 / Rsym value: 0.3 / % possible all: 76.2

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.488 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21716 5734 5 %RANDOM
Rwork0.19697 ---
all0.19796 108793 --
obs0.19796 108793 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-1.09 Å2
2---0.66 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8031 0 404 486 8921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0348605
X-RAY DIFFRACTIONr_angle_refined_deg1.2652.02111712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05951044
X-RAY DIFFRACTIONr_chiral_restr0.0870.21409
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026040
X-RAY DIFFRACTIONr_nbd_refined0.1850.24822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2667
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.218
X-RAY DIFFRACTIONr_mcbond_it0.3341.55192
X-RAY DIFFRACTIONr_mcangle_it0.66628351
X-RAY DIFFRACTIONr_scbond_it1.10433413
X-RAY DIFFRACTIONr_scangle_it1.8794.53361
LS refinement shellResolution: 1.8→1.843 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 324
Rwork0.25 6068

+
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