[English] 日本語
Yorodumi
- PDB-1zbq: Crystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogenase T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zbq
TitleCrystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogenase Type 4 In Complex With NAD
Components17-beta-hydroxysteroid dehydrogenase 4
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE / HYDROXYSTEROID DEHYDROGENASE / PEROXISOMAL BETA-OXIDATION / HUMAN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / medium-chain fatty-acyl-CoA metabolic process / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity ...3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / medium-chain fatty-acyl-CoA metabolic process / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / very long-chain fatty acid metabolic process / 3-hydroxyacyl-CoA dehydrogenase activity / Sertoli cell development / estradiol 17-beta-dehydrogenase [NAD(P)] activity / enoyl-CoA hydratase activity / peroxisomal membrane / estrogen metabolic process / fatty acid beta-oxidation / peroxisomal matrix / androgen metabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / isomerase activity / Peroxisomal protein import / osteoblast differentiation / peroxisome / protein homodimerization activity / membrane / cytosol
Similarity search - Function
Helix Hairpins - #4290 / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / short chain dehydrogenase / PKS_KR / HotDog domain superfamily / Short-chain dehydrogenase/reductase, conserved site ...Helix Hairpins - #4290 / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / short chain dehydrogenase / PKS_KR / HotDog domain superfamily / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Peroxisomal multifunctional enzyme type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLukacik, P. / Shafqat, N. / Kavanagh, K. / Bray, J. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogenase Type 4 In Complex With NAD
Authors: Lukacik, P. / Shafqat, N. / Kavanagh, K. / Bray, J. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Oppermann, U.
History
DepositionApr 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Aug 23, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 2RESOLUTION. 2.71 ANGSTROMS

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase 4
B: 17-beta-hydroxysteroid dehydrogenase 4
C: 17-beta-hydroxysteroid dehydrogenase 4
D: 17-beta-hydroxysteroid dehydrogenase 4
E: 17-beta-hydroxysteroid dehydrogenase 4
F: 17-beta-hydroxysteroid dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,55312
Polymers213,5726
Non-polymers3,9816
Water6,179343
1
A: 17-beta-hydroxysteroid dehydrogenase 4
B: 17-beta-hydroxysteroid dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5184
Polymers71,1912
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
ΔGint-84 kcal/mol
Surface area21670 Å2
MethodPISA
2
C: 17-beta-hydroxysteroid dehydrogenase 4
D: 17-beta-hydroxysteroid dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5184
Polymers71,1912
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-85 kcal/mol
Surface area21940 Å2
MethodPISA
3
E: 17-beta-hydroxysteroid dehydrogenase 4
F: 17-beta-hydroxysteroid dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5184
Polymers71,1912
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-86 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.826, 50.771, 183.775
Angle α, β, γ (deg.)87.52, 87.07, 70.75
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 3 - 304 / Label seq-ID: 24 - 325

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsThe biological assembly is a dimer

-
Components

#1: Protein
17-beta-hydroxysteroid dehydrogenase 4 / D-bifunctional protein / DBP / Peroxisomal multifunctional enzyme type 2 / MFE-2 / 17-beta-HSD 4 / ...D-bifunctional protein / DBP / Peroxisomal multifunctional enzyme type 2 / MFE-2 / 17-beta-HSD 4 / 3-hydroxyacyl-CoA dehydrogenase


Mass: 35595.348 Da / Num. of mol.: 6 / Fragment: N-terminal SHORT CHAIN DEHYDROGENASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B4, EDH17B4 / Plasmid: P11 (TORONTO) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P51659, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.1 Å3/Da / Density % sol: 40.8 %
Description: The completeness of 2.99-2.71 shell was 93.7%. The overall data completeness range ( 50.57- 2.71 Ang ) is 95.8. The overall data completeness range ( 50.57- 2.19 Ang) is 76.2.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium Sulphate monohydrate, 0.1M TRIS hydrochloride pH8.5, 30% w/v polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2005
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.19→50.574 Å / Num. all: 64535 / Num. obs: 64535 / % possible obs: 76.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.19→2.247 Å / % possible all: 29.71

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GZ6

1gz6


Resolution: 2.19→50.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.192 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.62 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALTHOUGH DATA COMPLETENESS FELL OFF AFTER 2.71 A, THERE WAS SIGNIFICANT DATA THAT EXTENDED TO 2.19 A. THE FULL RESOLUTION RANGE EXTENDING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALTHOUGH DATA COMPLETENESS FELL OFF AFTER 2.71 A, THERE WAS SIGNIFICANT DATA THAT EXTENDED TO 2.19 A. THE FULL RESOLUTION RANGE EXTENDING TO 2.19 A WAS USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.23568 3383 5 %RANDOM
Rwork0.18812 ---
obs0.1905 64535 76.23 %-
all-64535 --
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: 38.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å2-0.03 Å24.08 Å2
2--1.35 Å2-1.71 Å2
3----4.38 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13513 0 264 343 14120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02114119
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.96519174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00651824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11823.231588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.561152242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.35415118
X-RAY DIFFRACTIONr_chiral_restr0.0930.22144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210658
X-RAY DIFFRACTIONr_nbd_refined0.1990.26476
X-RAY DIFFRACTIONr_nbtor_refined0.2980.29623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2647
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.26
X-RAY DIFFRACTIONr_mcbond_it0.4511.59209
X-RAY DIFFRACTIONr_mcangle_it0.746214201
X-RAY DIFFRACTIONr_scbond_it1.40935706
X-RAY DIFFRACTIONr_scangle_it2.1894.54965
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1200tight positional0.040.05
2B1200tight positional0.040.05
3C1200tight positional0.050.05
4D1200tight positional0.040.05
5E1200tight positional0.040.05
6F1200tight positional0.040.05
1A943medium positional0.320.5
2B943medium positional0.310.5
3C943medium positional0.290.5
4D943medium positional0.30.5
5E943medium positional0.360.5
6F943medium positional0.320.5
1A1200tight thermal0.10.5
2B1200tight thermal0.10.5
3C1200tight thermal0.10.5
4D1200tight thermal0.110.5
5E1200tight thermal0.090.5
6F1200tight thermal0.090.5
1A943medium thermal0.632
2B943medium thermal0.682
3C943medium thermal0.682
4D943medium thermal0.712
5E943medium thermal0.62
6F943medium thermal0.572
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 82 -
Rwork0.29 1863 -
obs--29.71 %
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)
10.8301-0.1422-0.36091.53031.11433.4065-0.00070.1027-0.0454-0.11640.0596-0.0717-0.0684-0.0543-0.0588-0.27920.0077-0.0298-0.15320.0205-0.080325.618914.2604-43.7028
21.0338-0.3126-0.57681.84791.28763.01670.0591-0.07730.05750.14240.0098-0.0272-0.0949-0.028-0.0689-0.25180.0225-0.0662-0.16210.0338-0.100121.65622.5209-25.3915
30.9418-0.3923-0.69361.45040.94533.18460.06750.04850.0438-0.21360.0557-0.05910.05370.1857-0.1232-0.16290.0223-0.068-0.20430.0426-0.096.538327.0339-105.1275
40.8695-0.2981-0.44881.3890.8013.68430.0599-0.07510.06770.0590.0350.0649-0.02380.077-0.095-0.2309-0.0106-0.034-0.22960.0375-0.08390.751833.5057-86.6945
51.1075-0.0844-0.02491.56920.2284.39970.11650.0973-0.183-0.15360.18780.00750.5749-0.2612-0.3043-0.1150.0128-0.1207-0.13420.0517-0.044431.1652-6.774917.9199
61.4042-0.0973-0.56791.4904-0.01554.61250.0643-0.06340.00540.180.24810.1958-0.0599-0.744-0.3124-0.1890.0819-0.0495-0.01980.1327-0.058424.61512.36534.7547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 30424 - 325
2X-RAY DIFFRACTION2BB3 - 30424 - 325
3X-RAY DIFFRACTION3CC3 - 30424 - 325
4X-RAY DIFFRACTION4DD3 - 30424 - 325
5X-RAY DIFFRACTION5EE3 - 30424 - 325
6X-RAY DIFFRACTION6FF3 - 30424 - 325

+
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