[English] 日本語
Yorodumi
- PDB-5wqm: Crystal structure of a carbonyl reductase from Pseudomonas aerugi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wqm
TitleCrystal structure of a carbonyl reductase from Pseudomonas aeruginosa PAO1 (condition I)
ComponentsProbable dehydrogenase
KeywordsOXIDOREDUCTASE / short chain dehydrogenase/reductase
Function / homology
Function and homology information


carbonyl reductase (NADPH) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
: / short chain dehydrogenase / 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
Probable dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, S. / Wang, Y. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570128 China
CitationJournal: FEBS Lett. / Year: 2017
Title: Structure and characterization of a NAD(P)H-dependent carbonyl reductase from Pseudomonas aeruginosa PAO1.
Authors: Li, S. / Teng, X. / Su, L. / Mao, G. / Xu, Y. / Li, T. / Liu, R. / Zhang, Q. / Wang, Y. / Bartlam, M.
History
DepositionNov 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / 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
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable dehydrogenase
B: Probable dehydrogenase
C: Probable dehydrogenase
D: Probable dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4096
Polymers97,3634
Non-polymers462
Water1,58588
1
A: Probable dehydrogenase
C: Probable dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7274
Polymers48,6812
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-40 kcal/mol
Surface area17550 Å2
MethodPISA
2
B: Probable dehydrogenase
D: Probable dehydrogenase


Theoretical massNumber of molelcules
Total (without water)48,6812
Polymers48,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-30 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.150, 109.150, 142.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-301-

NA

21C-425-

HOH

31D-312-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 1 - 229 / Label seq-ID: 1 - 229

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Probable dehydrogenase


Mass: 24340.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4079 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HWU9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4M sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 27161 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rpim(I) all: 0.03 / Net I/σ(I): 24.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1291 / Rpim(I) all: 0.299 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXB

3wxb


Resolution: 2.6→43.35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 24.383 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.327
RfactorNum. reflection% reflectionSelection details
Rfree0.23304 1981 7.5 %RANDOM
Rwork0.18992 ---
obs0.19317 24428 97.23 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 53.153 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å2-0 Å2
2--0.35 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.6→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 2 88 6622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0146636
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176012
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.6388992
X-RAY DIFFRACTIONr_angle_other_deg0.8241.62314040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70620.87368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8471568
X-RAY DIFFRACTIONr_chiral_restr0.0550.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021180
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8952.0263480
X-RAY DIFFRACTIONr_mcbond_other1.8952.0263479
X-RAY DIFFRACTIONr_mcangle_it3.1113.0354336
X-RAY DIFFRACTIONr_mcangle_other3.1113.0354337
X-RAY DIFFRACTIONr_scbond_it2.212.3423156
X-RAY DIFFRACTIONr_scbond_other2.212.3423156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.583.4054656
X-RAY DIFFRACTIONr_long_range_B_refined6.00724.4016994
X-RAY DIFFRACTIONr_long_range_B_other624.386990
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A64720.1
12B64720.1
21A65200.09
22C65200.09
31A65460.09
32D65460.09
41B65060.09
42C65060.09
51B65110.09
52D65110.09
61C65830.09
62D65830.09
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 130 -
Rwork0.263 1595 -
obs--88.28 %
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)
12.92390.5146-0.04134.1159-0.01521.3056-0.0001-0.03570.7366-0.37620.1842-0.6349-0.28360.3897-0.18410.1255-0.09480.17320.2155-0.11570.511533.629-44.686-13.854
23.824-1.41130.74364.9374-1.50861.9464-0.0047-0.87240.78610.39020.3136-0.4708-0.3070.3023-0.30890.0783-0.06570.09160.4206-0.32030.449131.637-43.018-0.046
34.13750.85180.00714.1864-0.27862.09560.1127-0.68530.4990.04170.0067-0.7541-0.23250.3561-0.11940.229-0.07130.10950.2556-0.08060.410111.247-21.405-18.967
45.9675-1.06070.0133.674-1.16422.6441-0.10860.34690.4136-1.14760.073-0.83890.09940.24760.03560.4515-0.09220.24990.13330.04040.322414.391-23.147-32.561
53.59350.7352-1.16524.31080.571.8831-0.16880.118-0.4875-0.30670.08180.30850.3251-0.00950.0870.12630.0140.01360.07250.00660.259215.019-72.236-14.126
64.276-0.9672-1.15972.62320.91683.8092-0.1938-0.5641-0.58220.64960.12670.20520.58470.67820.06710.24570.1180.10590.2780.09930.211818.038-75.56-0.718
73.31011.66890.47933.35121.1511.75210.1674-0.5702-0.10010.1943-0.13530.57720.0403-0.3196-0.03220.24760.02050.01360.18610.14020.3273-16.428-39.734-21.515
85.72810.8016-0.28635.71172.41162.0033-0.00150.07420.0914-0.6484-0.1080.642-0.4729-0.05510.10950.37490.0094-0.08160.06710.07620.2283-18.546-36.303-35.149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 183
2X-RAY DIFFRACTION2A195 - 229
3X-RAY DIFFRACTION3B1 - 183
4X-RAY DIFFRACTION4B195 - 229
5X-RAY DIFFRACTION5C1 - 183
6X-RAY DIFFRACTION6C195 - 229
7X-RAY DIFFRACTION7D1 - 183
8X-RAY DIFFRACTION8D195 - 229

+
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