[English] 日本語
Yorodumi
- PDB-3tl3: Structure of a short-chain type dehydrogenase/reductase from Myco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tl3
TitleStructure of a short-chain type dehydrogenase/reductase from Mycobacterium ulcerans
ComponentsShort-chain type dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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
Short-chain type dehydrogenase/reductase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
DepositionAug 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 / 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_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 type dehydrogenase/reductase
B: Short-chain type dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2343
Polymers53,2112
Non-polymers231
Water5,044280
1
A: Short-chain type dehydrogenase/reductase
B: Short-chain type dehydrogenase/reductase
hetero molecules

A: Short-chain type dehydrogenase/reductase
B: Short-chain type dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4686
Polymers106,4224
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area9770 Å2
ΔGint-95 kcal/mol
Surface area33580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.946, 73.245, 109.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Short-chain type dehydrogenase/reductase


Mass: 26605.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: MUL_0987 / Production host: Escherichia coli (E. coli) / References: UniProt: A0PMN1, Oxidoreductases
#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 / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25.7 mg/mL MyulA.00554.a.A1 PS00974. 0.1 M MMT buffer, pH 8.0, 25% PEG1500, cryoprotection 20% ethylene glycol , VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 38385 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.082 / Χ2: 1.037 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.884.90.43518961.085199
1.88-1.924.80.39118421.076198.7
1.92-1.954.80.33218971.07199.1
1.95-1.994.90.27118741.055198.9
1.99-2.044.90.23619151.044199.4
2.04-2.084.90.20918651.072199.5
2.08-2.144.90.17618921.05199.5
2.14-2.194.90.14619001.029199.1
2.19-2.264.80.14918831.018199.7
2.26-2.334.90.13318941.034199.3
2.33-2.414.80.11119190.998199.7
2.41-2.514.80.10419241.003199.6
2.51-2.634.80.09919110.994199.7
2.63-2.764.80.08719140.95199.7
2.76-2.944.80.07619310.991199.8
2.94-3.164.80.07319321.06199.8
3.16-3.484.70.06619541.053199.7
3.48-3.994.60.05819621.038199.9
3.99-5.024.60.04619911.064199.7
5.02-504.50.05520891.064199.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.11 Å
Translation2.5 Å49.11 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UAY

1uay


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2129 / WRfactor Rwork: 0.1838 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8789 / SU B: 4.988 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1369 / SU Rfree: 0.1221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 1914 5 %RANDOM
Rwork0.1774 ---
obs0.1788 38188 98.92 %-
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 max: 63.15 Å2 / Biso mean: 21.8065 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 1 280 3591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193389
X-RAY DIFFRACTIONr_bond_other_d0.0010.022159
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9754624
X-RAY DIFFRACTIONr_angle_other_deg0.91435301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67523.719121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89515511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9621528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 140 -
Rwork0.208 2390 -
all-2530 -
obs--96.34 %
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)
11.4565-0.0675-0.02871.67320.00291.52340.02970.00860.0214-0.184-0.0125-0.07320.04420.0859-0.01710.06880.0090.00950.0407-0.00750.0202-14.0987-19.9726-24.5804
23.23881.3973-0.16811.50120.43760.80770.12460.08490.0383-0.0869-0.0382-0.0124-0.0360.0047-0.08650.10160.0161-0.00180.07740.02120.0636-16.8097-6.995-21.9015
33.21522.5112-0.51873.183-0.3580.75720.0381-0.00750.0755-0.00830.0201-0.0975-0.0869-0.0036-0.05820.08110.00230.00210.0712-0.00010.0537-16.0406-6.2607-12.6614
41.36810.1520.61390.9243-0.0651.4853-0.02440.1307-0.0163-0.0348-0.0159-0.1342-0.02180.24640.04030.0687-0.00240.00540.09170.01090.0526-8.5248-14.7573-8.4096
51.443-0.0109-0.00751.4668-0.09271.0962-0.0340.04940.0613-0.1488-0.01470.0258-0.075-0.05450.04870.0864-0.0067-0.01260.04570.02980.0357-14.048625.0517-17.9617
64.0932.87071.06883.81931.03751.61940.04030.1391-0.114-0.1030.0263-0.1233-0.04270.0652-0.06660.09470.00960.02320.07490.0090.0485-7.585313.3127-18.3534
71.26160.66920.78281.82050.80381.54270.0291-0.0487-0.0279-0.0798-0.07360.2250.0928-0.08810.04450.0622-0.00160.00660.04710.01270.0605-14.54199.3794-10.5983
81.71760.0149-0.29360.6268-0.09211.1285-0.00630.0834-0.0399-0.0622-0.00570.0565-0.0017-0.15160.01190.0724-0.0031-0.00060.07130.00040.0447-19.828815.7781-4.5852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 93
2X-RAY DIFFRACTION2A94 - 135
3X-RAY DIFFRACTION3A136 - 176
4X-RAY DIFFRACTION4A177 - 248
5X-RAY DIFFRACTION5B5 - 90
6X-RAY DIFFRACTION6B99 - 135
7X-RAY DIFFRACTION7B136 - 174
8X-RAY DIFFRACTION8B175 - 248

+
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