[English] 日本語
Yorodumi
- PDB-3o38: Crystal structure of a short chain dehydrogenase from Mycobacteri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o38
TitleCrystal structure of a short chain dehydrogenase from Mycobacterium smegmatis
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / Mycobacterium / tuberculosis / ortholog from a non-pathogenic species / dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / oxidoreductase activity / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Short chain dehydrogenase
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: 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
DepositionJul 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 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_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_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.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_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_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_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: Short chain dehydrogenase
B: Short chain dehydrogenase
C: Short chain dehydrogenase
D: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7665
Polymers112,7434
Non-polymers231
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15190 Å2
ΔGint-106 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.810, 75.720, 80.030
Angle α, β, γ (deg.)90.000, 102.710, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Short chain dehydrogenase


Mass: 28185.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6011 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R4Z8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 53.4 mg/mL MysmA00762bA1 PS00603 against PACT B2, 0.1 M MIB buffer, 25% PEG 1500, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 64541 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 28.324 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.3552.910615395181
2-2.060.2933.812733432691
2.06-2.120.2534.915158453198.2
2.12-2.180.2096.215709441798.6
2.18-2.250.169817247435499.6
2.25-2.330.1529.1173044182100
2.33-2.420.1261116867406499.7
2.42-2.520.1061316309392599.7
2.52-2.630.09115.115560373499.9
2.63-2.760.07817.115012360299.8
2.76-2.910.06221.114117340399.7
2.91-3.080.05225.113389324099.9
3.08-3.30.04329.912550304799.7
3.3-3.560.03237.511503282099.7
3.56-3.90.02842.110557261199.5
3.9-4.360.02545.69499237099.7
4.36-5.030.02447.78366209299.6
5.03-6.170.02644.57137178599.8
6.17-8.720.02150.25441137399.3
8.720.01955.5269871490

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.06 Å19.55 Å
Translation2.06 Å19.55 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1iy8

1iy8


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2009 / WRfactor Rwork: 0.1522 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8751 / SU B: 8.143 / SU ML: 0.104 / SU R Cruickshank DPI: 0.166 / SU Rfree: 0.1537 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 3265 5.1 %RANDOM
Rwork0.1624 ---
obs0.165 64451 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 148.6 Å2 / Biso mean: 29.2692 Å2 / Biso min: 10.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å20.4 Å2
2---0.11 Å20 Å2
3---1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7091 0 1 670 7762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0217233
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9459854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7585979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81823.163294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.204151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4651566
X-RAY DIFFRACTIONr_chiral_restr0.0920.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025444
X-RAY DIFFRACTIONr_mcbond_it0.7641.54796
X-RAY DIFFRACTIONr_mcangle_it1.30527635
X-RAY DIFFRACTIONr_scbond_it2.21832437
X-RAY DIFFRACTIONr_scangle_it3.6494.52210
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 190 -
Rwork0.214 3746 -
all-3936 -
obs--80.87 %
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)
10.78750.10460.02820.062-0.05390.25240.0147-0.09160.0632-0.0269-0.02450.0130.01590.03660.00980.0635-0.00350.00720.0284-0.02120.05960.493736.854374.1212
20.8352-0.047-0.0320.0037-0.00990.13330.0084-0.06020.1489-0.00440.0105-0.00490.0411-0.0427-0.0190.0590.00060.00760.025-0.0070.098926.984738.519771.1313
30.67160.02180.12750.03930.05480.1086-0.01930.21510.05060.02620.00710.0210.03940.01630.01220.057-0.0121-0.0160.10520.04550.050830.842935.11941.5991
40.61180.2861-0.07750.1549-0.07580.1252-0.06520.18140.1406-0.01040.05290.05930.01490.06330.01230.0738-0.0216-0.00180.11910.06290.042163.41742.832845.0753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

+
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