[English] 日本語
Yorodumi
- PDB-3s55: Crystal structure of a putative short-chain dehydrogenase/reducta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s55
TitleCrystal structure of a putative short-chain dehydrogenase/reductase from Mycobacterium abscessus bound to NAD
ComponentsPutative short-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ortholog / SDR
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Mycofactocin-dependent oxidoreductase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative short-chain dehydrogenase/reductase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Sci Rep / Year: 2017
Title: Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors.
Authors: Haft, D.H. / Pierce, P.G. / Mayclin, S.J. / Sullivan, A. / Gardberg, A.S. / Abendroth, J. / Begley, D.W. / Phan, I.Q. / Staker, B.L. / Myler, P.J. / Marathias, V.M. / Lorimer, D.D. / Edwards, T.E.
#1: Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Sep 13, 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_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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 / _struct_ref_seq_dif.details / _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: Putative short-chain dehydrogenase/reductase
B: Putative short-chain dehydrogenase/reductase
C: Putative short-chain dehydrogenase/reductase
D: Putative short-chain dehydrogenase/reductase
E: Putative short-chain dehydrogenase/reductase
F: Putative short-chain dehydrogenase/reductase
G: Putative short-chain dehydrogenase/reductase
H: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,89524
Polymers235,2678
Non-polymers5,62816
Water22,5911254
1
A: Putative short-chain dehydrogenase/reductase
B: Putative short-chain dehydrogenase/reductase
C: Putative short-chain dehydrogenase/reductase
D: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,44712
Polymers117,6334
Non-polymers2,8148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18150 Å2
ΔGint-167 kcal/mol
Surface area32130 Å2
MethodPISA
2
E: Putative short-chain dehydrogenase/reductase
F: Putative short-chain dehydrogenase/reductase
G: Putative short-chain dehydrogenase/reductase
H: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,44712
Polymers117,6334
Non-polymers2,8148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18140 Å2
ΔGint-166 kcal/mol
Surface area32110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.360, 84.970, 100.890
Angle α, β, γ (deg.)81.770, 76.780, 74.230
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11F
21A
31B
41C
51D
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 4 - 278 / Label seq-ID: 7 - 281

Dom-IDAuth asym-IDLabel asym-ID
1FF
2AA
3BB
4CC
5DD
6FF
7GG
8HH

-
Components

#1: Protein
Putative short-chain dehydrogenase/reductase


Mass: 29408.330 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_1408c / Production host: Escherichia coli (E. coli) / References: UniProt: B1MLR7
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1254 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MyabA.01326.f.A1 PW30378 at 27.3 mg/mL against JCSG+ screen condition D10, 0.2 M Ca(OAc)2, 0.1 M Na cacodylate pH 6.5, 40% PEG 300, direct cryo, crsytal tracking ID 219629d10, VAPOR ...Details: MyabA.01326.f.A1 PW30378 at 27.3 mg/mL against JCSG+ screen condition D10, 0.2 M Ca(OAc)2, 0.1 M Na cacodylate pH 6.5, 40% PEG 300, direct cryo, crsytal tracking ID 219629d10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 125503 / Num. obs: 119101 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 18.864 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.1-2.153.60.2495.59291609192821089.3
2.15-2.210.2376.3133201842092.7
2.21-2.280.2356.631420812192
2.28-2.350.1967.3331803802293.6
2.35-2.420.1827.830775775393.8
2.42-2.510.1847.5429983754094.3
2.51-2.60.1678.0429277736294.9
2.6-2.710.1558.5328177711495
2.71-2.830.1398.9227005677595.5
2.83-2.970.11510.2125974651995.8
2.97-3.130.09711.5625194632296.4
3.13-3.320.08512.9523443588896.5
3.32-3.550.07316.0122099559596.9
3.55-3.830.06319.4520391522597.2
3.83-4.20.05720.7618767479097
4.2-4.70.05222.6717020435497.6
4.7-5.420.06118.6115351388698.4
5.42-6.640.07914.2812953326599
6.64-9.390.0521.2510070255899.3
9.390.03828.775280138298.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.76 Å
Translation2.5 Å45.76 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3oec

3oec


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.2087 / WRfactor Rwork: 0.1675 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8391 / SU B: 10.696 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2591 / SU Rfree: 0.2018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 5974 5 %RANDOM
Rwork0.1893 ---
obs0.1917 119100 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.03 Å2 / Biso mean: 12.2523 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.18 Å2-0.39 Å2
2--0.4 Å20.38 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15649 0 360 1254 17263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216373
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.98122411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16352184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0724.505586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.639152432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9131577
X-RAY DIFFRACTIONr_chiral_restr0.0930.22746
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112121
X-RAY DIFFRACTIONr_mcbond_it0.6281.510747
X-RAY DIFFRACTIONr_mcangle_it1.1217196
X-RAY DIFFRACTIONr_scbond_it1.90235626
X-RAY DIFFRACTIONr_scangle_it3.0084.55198
Refine LS restraints NCS

Ens-ID: 1 / Number: 1867 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1FLOOSE POSITIONAL0.235
2ALOOSE POSITIONAL0.285
3BLOOSE POSITIONAL0.295
4CLOOSE POSITIONAL0.255
5DLOOSE POSITIONAL0.225
6FLOOSE POSITIONAL0.235
7GLOOSE POSITIONAL0.35
8HLOOSE POSITIONAL0.245
1FLOOSE THERMAL1.8110
2ALOOSE THERMAL1.9310
3BLOOSE THERMAL1.5310
4CLOOSE THERMAL1.410
5DLOOSE THERMAL1.7310
6FLOOSE THERMAL1.8110
7GLOOSE THERMAL1.6110
8HLOOSE THERMAL1.5710
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 414 -
Rwork0.198 7780 -
all-8194 -
obs--89.31 %
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)
10.27330.021-0.00090.3253-0.04040.55950.01410.010.02820.0405-0.00460.0153-0.0580.0852-0.00950.0217-0.0114-0.00950.0175-0.00160.016947.9524-14.983950.0718
20.3432-0.04740.0850.1898-0.08530.55420.00750.0402-0.0533-0.00420.00080.01470.00510.0694-0.00840.00430.0052-0.00360.0209-0.01110.012446.7309-29.405121.9794
30.3857-0.05080.17820.20510.05020.4843-0.02320.01240.0092-0.00710.0079-0.0008-0.0277-0.04140.01530.00950.0057-0.00920.0129-0.00250.013414.5863-22.250822.4722
40.25240.0653-0.00140.2068-0.01770.58830.0084-0.0217-0.027-0.0023-0.0149-0.0017-0.0039-0.0610.00660.00240.00380.00030.01830.00390.009516.8278-24.994553.7053
50.3044-0.0528-0.03130.5152-0.14580.46660.01460.02720.0141-0.0287-0.00120.05990.06820.0134-0.01340.0226-0.0063-0.00490.0102-0.00020.013139.0528-0.2889-14.8288
60.26720.0893-0.0620.4375-0.06970.33640.0146-0.03240.06740.0108-0.00290.049-0.00240.0135-0.01170.00530.00140.00540.006-0.00540.02540.277930.3987-8.5183
70.2860.1305-0.09250.3651-0.07160.3051-0.0050.00350.0092-0.0211-0.0018-0.02680.00330.00380.00680.00660.00080.00590.0138-0.00180.012772.487228.1086-16.0819
80.25050.09340.03350.4435-0.02560.3193-0.0128-0.0342-0.0184-0.0131-0.0114-0.06710.0049-0.01090.02410.01260.0102-0.00280.0098-0.00150.01870.2936-1.3489-4.9977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 278
2X-RAY DIFFRACTION1A279
3X-RAY DIFFRACTION2B4 - 278
4X-RAY DIFFRACTION2B279
5X-RAY DIFFRACTION3C3 - 278
6X-RAY DIFFRACTION3C279
7X-RAY DIFFRACTION4D4 - 278
8X-RAY DIFFRACTION4D279
9X-RAY DIFFRACTION5E3 - 278
10X-RAY DIFFRACTION5E279
11X-RAY DIFFRACTION6F4 - 278
12X-RAY DIFFRACTION6F279
13X-RAY DIFFRACTION7G3 - 278
14X-RAY DIFFRACTION7G279
15X-RAY DIFFRACTION8H4 - 278
16X-RAY DIFFRACTION8H279

+
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://pdbjlvh1.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