[English] 日本語
Yorodumi
- PDB-3qiv: Crystal structure of a putative short-chain dehydrogenase or 3-ox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qiv
TitleCrystal structure of a putative short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase from Mycobacterium paratuberculosis ATCC BAA-968 / K-10
Componentsshort-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / NADB_Rossman superfamily
Function / homology
Function and homology information


fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / 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 dehydrogenase
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase
B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)53,3432
Polymers53,3432
Non-polymers00
Water2,144119
1
A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase
B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase

A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase
B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)106,6854
Polymers106,6854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6640 Å2
ΔGint-33 kcal/mol
Surface area31700 Å2
MethodPISA
2
A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase

A: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)53,3432
Polymers53,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2300 Å2
ΔGint-11 kcal/mol
Surface area17250 Å2
MethodPISA
3
B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase

B: short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)53,3432
Polymers53,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1980 Å2
ΔGint-9 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.440, 90.070, 92.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 26671.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: MAP_0603 / Production host: Escherichia coli (E. coli) / References: UniProt: Q743I2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 16.94 mg/ml MypaA.00414.c.A1, 300 mM magnessium formate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2010
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 24019 / % possible obs: 99.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.055 / Χ2: 1 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.294.20.35211831.043199.7
2.29-2.334.70.24411720.949199.5
2.33-2.384.80.18711970.905199.8
2.38-2.424.80.18411720.916199.9
2.42-2.484.80.1412040.97199.8
2.48-2.534.80.13911801.009199.7
2.53-2.64.80.12211950.978199.7
2.6-2.674.80.10911830.978199.6
2.67-2.754.80.10212051.035199.4
2.75-2.834.80.08312011.035199.7
2.83-2.944.80.07111861.011199.6
2.94-3.054.80.05911931.075199.4
3.05-3.194.80.05211951.045199.4
3.19-3.364.80.04811930.992198.8
3.36-3.574.80.04512110.995199.3
3.57-3.854.70.04712120.96198.7
3.85-4.234.60.05512101.085198.6
4.23-4.854.40.04912021.076197.6
4.85-6.14.50.04612370.991197.9
6.1-504.50.0212880.963195.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.47 Å
Translation2.5 Å40.47 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GVC

3gvc


Resolution: 2.25→40.47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2452 / WRfactor Rwork: 0.2144 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.827 / SU B: 12.298 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2567 / SU Rfree: 0.2121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 1221 5.1 %RANDOM
Rwork0.2153 ---
obs0.2173 23922 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.35 Å2 / Biso mean: 36.868 Å2 / Biso min: 2.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 0 119 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222857
X-RAY DIFFRACTIONr_bond_other_d0.0010.021825
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.9553864
X-RAY DIFFRACTIONr_angle_other_deg0.80634470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97225.135111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0581514
X-RAY DIFFRACTIONr_chiral_restr0.050.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02559
X-RAY DIFFRACTIONr_mcbond_it0.3421.51925
X-RAY DIFFRACTIONr_mcbond_other0.051.5825
X-RAY DIFFRACTIONr_mcangle_it0.6523014
X-RAY DIFFRACTIONr_scbond_it0.9413932
X-RAY DIFFRACTIONr_scangle_it1.5884.5850
LS refinement shellResolution: 2.247→2.306 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 74 -
Rwork0.392 1623 -
all-1697 -
obs--96.81 %
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)
14.3004-0.3549-1.25675.42520.47046.0243-0.00490.1267-0.29280.1431-0.16170.46640.1736-0.79590.16660.1167-0.01590.01790.1642-0.04870.16895.59238.82314.27
21.828-0.562-2.20730.22280.44635.28220.14680.210.2171-0.0649-0.0505-0.0194-0.2872-0.4241-0.09630.20880.02020.02270.09530.00310.202215.02345.5287.051
35.6504-0.1041-0.47534.58110.77783.1347-0.04570.1261-0.3357-0.1684-0.04970.15320.4312-0.06250.09540.2458-0.02350.02030.0313-0.01230.141718.22332.12614.97
44.435-0.2884-0.22822.2870.47142.93440.0283-0.6508-0.24620.12440.1102-0.03010.00790.0771-0.13850.1096-0.02580.0050.1930.05920.155818.2230.1723.198
516.311-0.1939-6.1680.02090.0632.34020.1475-0.86270.2414-0.0013-0.05040.0235-0.04070.3671-0.09710.17730.0050.01440.3034-0.00910.157833.5981.436.217
63.87260.4859-0.32984.11150.01824.37110.15940.02930.29710.05110.0686-0.1008-0.38750.1212-0.2280.164-0.0180.04320.09730.01430.175815.34812.43513.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 26
2X-RAY DIFFRACTION2A27 - 128
3X-RAY DIFFRACTION3A129 - 241
4X-RAY DIFFRACTION4B0 - 89
5X-RAY DIFFRACTION5B90 - 125
6X-RAY DIFFRACTION6B126 - 242

+
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