[English] 日本語
Yorodumi
- PDB-4jbi: 2.35A resolution structure of NADPH bound thermostable alcohol de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jbi
Title2.35A resolution structure of NADPH bound thermostable alcohol dehydrogenase from Pyrobaculum aerophilum
ComponentsAlcohol dehydrogenase (Zinc)
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / thermostability / Zinc binding / NADPH
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Alcohol dehydrogenase (Zinc)
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsLovell, S. / Battaile, K.P. / Vitale, A. / Throne, N. / Hu, X. / Shen, M. / D'Auria, S. / Auld, D.S.
CitationJournal: Plos One / Year: 2013
Title: Physicochemical Characterization of a Thermostable Alcohol Dehydrogenase from Pyrobaculum aerophilum.
Authors: Vitale, A. / Thorne, N. / Lovell, S. / Battaile, K.P. / Hu, X. / Shen, M. / D'Auria, S. / Auld, D.S.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 22, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop ...pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_struct_assembly_prop.value / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Alcohol dehydrogenase (Zinc)
B: Alcohol dehydrogenase (Zinc)
C: Alcohol dehydrogenase (Zinc)
D: Alcohol dehydrogenase (Zinc)
E: Alcohol dehydrogenase (Zinc)
F: Alcohol dehydrogenase (Zinc)
G: Alcohol dehydrogenase (Zinc)
H: Alcohol dehydrogenase (Zinc)
I: Alcohol dehydrogenase (Zinc)
J: Alcohol dehydrogenase (Zinc)
K: Alcohol dehydrogenase (Zinc)
L: Alcohol dehydrogenase (Zinc)
M: Alcohol dehydrogenase (Zinc)
N: Alcohol dehydrogenase (Zinc)
O: Alcohol dehydrogenase (Zinc)
P: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)631,98648
Polymers619,01316
Non-polymers12,97332
Water19,9431107
1
A: Alcohol dehydrogenase (Zinc)
E: Alcohol dehydrogenase (Zinc)
F: Alcohol dehydrogenase (Zinc)
K: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99612
Polymers154,7534
Non-polymers3,2438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-49 kcal/mol
Surface area46320 Å2
MethodPISA
2
B: Alcohol dehydrogenase (Zinc)
C: Alcohol dehydrogenase (Zinc)
D: Alcohol dehydrogenase (Zinc)
L: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99612
Polymers154,7534
Non-polymers3,2438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-51 kcal/mol
Surface area46470 Å2
MethodPISA
3
G: Alcohol dehydrogenase (Zinc)
H: Alcohol dehydrogenase (Zinc)
N: Alcohol dehydrogenase (Zinc)
P: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99612
Polymers154,7534
Non-polymers3,2438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-49 kcal/mol
Surface area46060 Å2
MethodPISA
4
I: Alcohol dehydrogenase (Zinc)
J: Alcohol dehydrogenase (Zinc)
M: Alcohol dehydrogenase (Zinc)
O: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99612
Polymers154,7534
Non-polymers3,2438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-51 kcal/mol
Surface area45980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.133, 169.262, 149.151
Angle α, β, γ (deg.)90.000, 116.250, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Alcohol dehydrogenase (Zinc)


Mass: 38688.293 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea)
Strain: ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827
Gene: PAE2687 / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q8ZUP0, alcohol dehydrogenase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1107 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10%(w/v) PEG 8000, 100 mM Hepes, 8% (v/v) ethylene glycol, pH 7.5, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→133.767 Å / Num. all: 254725 / Num. obs: 254725 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.7 / Num. unique all: 12550 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHASERphasing
PHENIXdev_1241refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JBG

4jbg


Resolution: 2.35→44.589 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 12800 5.03 %RANDOM
Rwork0.1613 ---
obs0.1639 254638 99.89 %-
all-254638 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.66 Å2 / Biso mean: 43.351 Å2 / Biso min: 18.54 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38810 0 784 1107 40701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01140503
X-RAY DIFFRACTIONf_angle_d1.17255353
X-RAY DIFFRACTIONf_chiral_restr0.0766414
X-RAY DIFFRACTIONf_plane_restr0.0077112
X-RAY DIFFRACTIONf_dihedral_angle_d15.68214661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.37670.31563740.236380908464100
2.3767-2.40470.27183810.215580448425100
2.4047-2.4340.30954330.217280528485100
2.434-2.46480.26754420.209479998441100
2.4648-2.49720.27124380.208680548492100
2.4972-2.53140.28294250.205580708495100
2.5314-2.56760.27534380.201780268464100
2.5676-2.60590.28033970.190180688465100
2.6059-2.64660.27224410.191380248465100
2.6466-2.690.25514480.177979828430100
2.69-2.73640.24344370.172280338470100
2.7364-2.78610.23613910.170980948485100
2.7861-2.83970.23914530.176480368489100
2.8397-2.89770.25554860.182379858471100
2.8977-2.96070.25544210.178880588479100
2.9607-3.02950.25743950.182381008495100
3.0295-3.10530.23084270.173780468473100
3.1053-3.18920.23184400.172380508490100
3.1892-3.2830.23774400.170180318471100
3.283-3.3890.24524490.178680808529100
3.389-3.510.23034240.179180038427100
3.51-3.65050.23334340.169180708504100
3.6505-3.81660.20844220.170781108532100
3.8166-4.01770.19314220.148880708492100
4.0177-4.26920.18174160.133980708486100
4.2692-4.59850.15593980.121681108508100
4.5985-5.06070.14884260.11681008526100
5.0607-5.79160.15064270.124781258552100
5.7916-7.29170.17314260.132781248550100
7.2917-44.59710.14674490.13358134858399

+
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