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- PDB-3imf: 1.99 Angstrom resolution crystal structure of a short chain dehyd... -

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Basic information

Entry
Database: PDB / ID: 3imf
Title1.99 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor'
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


2,4-dienoyl-CoA reductase [(2E)-enoyl-CoA-producing] / 2,4-dienoyl-CoA reductase (NADPH) activity / :
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
ACETATE ION / 2,4-dienoyl-CoA reductase / Oxidoreductase, short chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHalavaty, A.S. / Minasov, G. / Skarina, T. / Onopriyenko, O. / Gordon, E. / Peterson, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.99 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor'
Authors: Halavaty, A.S. / Minasov, G. / Skarina, T. / Onopriyenko, O. / Gordon, E. / Peterson, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)113,7906
Polymers113,6724
Non-polymers1182
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-91.3 kcal/mol
Surface area35650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.237, 89.560, 71.785
Angle α, β, γ (deg.)90.00, 111.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Short chain dehydrogenase


Mass: 28418.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria)
Strain: Ames Ancestor / Gene: BAS3900, BA_4204, GBAA4204, GBAA_4204, YP_020848 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q81MP2, UniProt: A0A6L8NTZ6*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% MPD, 0.1M Mg Acetate, 50mM MES pH 5.6. For cryoprotection, 5% Glycerol, 5% Sucrose, 5% Ethylene glycol were used, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Beryllium lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. all: 136276 / Num. obs: 136276 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.79
Reflection shellResolution: 1.99→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.38 / Num. unique all: 6792 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1W8D
Resolution: 1.99→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.524 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20643 3494 5 %RANDOM
Rwork0.16609 ---
all0.16815 65695 --
obs0.16815 65695 98.83 %-
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 mean: 17.705 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å20 Å21.32 Å2
2---0.97 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.99→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7472 0 8 592 8072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227900
X-RAY DIFFRACTIONr_bond_other_d0.0010.025339
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.95310695
X-RAY DIFFRACTIONr_angle_other_deg0.816313106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.00551041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24224.924327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.809151422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3911543
X-RAY DIFFRACTIONr_chiral_restr0.0850.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021513
X-RAY DIFFRACTIONr_mcbond_it0.931.55037
X-RAY DIFFRACTIONr_mcbond_other0.2611.52114
X-RAY DIFFRACTIONr_mcangle_it1.65628094
X-RAY DIFFRACTIONr_scbond_it2.80332863
X-RAY DIFFRACTIONr_scangle_it4.5084.52601
LS refinement shellResolution: 1.99→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 240 -
Rwork0.169 4509 -
obs-4509 91.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
111.827-9.58512.446610.5786-9.552121.1930.68721.1107-1.003-0.9227-0.34670.92350.9314-0.8383-0.34050.3699-0.2207-0.21110.74460.00130.49240.9925-5.090515.5656
22.0668-0.0574-0.15751.4867-0.36982.2698-0.0153-0.07610.12440.1190.0060.1578-0.1498-0.2820.00940.01740.02650.00950.1301-0.01160.07895.96972.446129.0822
30.84980.11410.01470.75560.19370.9251-0.0491-0.062-0.00070.06220.04070.0619-0.0112-0.0840.00840.01740.01570.00430.02430.0130.030822.9826-0.654128.1481
45.15226.0273-9.27239.8576-10.818616.69611.17640.48190.8810.8730.42050.9214-2.0176-0.9321-1.59690.8676-0.1562-0.0590.59410.12181.527625.054525.365721.8538
51.39350.0248-0.63442.5631-1.08281.50130.06290.03880.14580.22390.00470.1192-0.2263-0.2582-0.06760.04810.0268-0.00570.08110.00020.045218.27686.503812.517
61.042-1.27-1.00432.5411-0.47733.8830.0289-0.0660.03810.02420.0441-0.0284-0.12710.1217-0.0730.07560.0104-0.02760.04950.0050.030731.206210.469413.1825
714.91077.6965-7.206613.4584-0.044818.6623-0.24790.09620.63780.57070.0531.3349-0.0957-1.33990.19490.19530.0825-0.02150.44740.00490.462911.15168.1486-6.992
81.87610.0508-0.11871.6890.17361.79250.02090.2554-0.1081-0.1707-0.01750.09920.1614-0.1794-0.00340.0771-0.0077-0.04880.13-0.01870.042722.5758-0.9425-13.5856
91.3077-0.81920.22071.3605-0.34870.40250.05110.0942-0.0179-0.1104-0.01010.02780.006-0.0072-0.0410.0284-0.006-0.01770.02240.00130.025435.67452.1378-1.5088
102.40540.36420.63020.3915-0.25750.5399-0.02590.2415-0.5221-0.22320.0191-0.22010.260.06880.00680.4299-0.04920.06280.2437-0.04820.334826.4299-13.35110.9941
116.3721-6.3175-0.65437.80958.593842.3830.17260.7162-0.67150.5782-0.15030.49993.55481.9235-0.02230.74010.20680.13330.4347-0.10261.052130.1575-26.27539.0397
120.85570.19820.06161.0288-0.38381.5318-0.0530.068-0.0856-0.14020.0266-0.01460.1402-0.12490.02640.0269-0.01330.00230.04540.00090.048223.0306-6.07859.4178
1324.880615.68628.600112.696812.297320.04831.2138-1.0558-1.05161.2998-0.4118-0.81741.36070.4988-0.8020.6275-0.0079-0.15550.47910.10260.384771.9507-8.343417.2501
141.7497-0.0055-0.02321.83630.23692.25180.02840.09080.1292-0.1106-0.0036-0.2391-0.17620.3621-0.02490.0191-0.02830.01670.130.00880.09668.190.72984.4621
151.3678-1.10710.60581.6705-0.47710.8364-0.00350.04210.1131-0.07010.0027-0.15510.01450.04490.00090.013-0.012-0.00520.02390.0090.039350.44540.82892.5336
161.28580.0385-0.00891.88190.68461.88420.03310.01610.0543-0.11280.0273-0.0285-0.26270.1073-0.06040.0381-0.0130.01020.0111-0.00170.020751.617-0.632812.6341
171.4562-0.4014-0.31432.27151.47271.53160.0584-0.03150.1092-0.11890.0736-0.1778-0.20330.2622-0.1320.064-0.0376-0.01010.0953-0.01120.055855.87193.839821.094
185.95081.9621-1.75792.4231.08236.10870.09060.00540.27760.0238-0.03840.0996-0.2706-0.2453-0.05210.0957-0.0184-0.02730.04650.00250.027242.905511.546421.1034
1919.9709-12.0429-3.307918.0378-5.612812.2259-0.04760.02711.0611-0.5342-0.0811-1.8311-0.91561.35330.12870.3798-0.24760.05920.4691-0.02820.462663.14536.46940.0829
202.0977-0.3933-0.13442.05040.20332.38990.0186-0.2479-0.1660.21140.0033-0.0840.08270.1713-0.02190.0846-0.0064-0.05620.14880.02080.049351.2719-2.606247.0918
211.6370.60350.27931.16910.41140.94620.0447-0.0639-0.05880.2010.0557-0.0224-0.02590.0165-0.10030.06290.0203-0.00620.04110.01320.038736.9025-1.396636.17
221.4531-1.1457-0.26294.7010.29841.7127-0.0446-0.1255-0.02960.1757-0.00930.04010.04830.06320.05390.03350.0001-0.00930.0296-0.00340.010945.15971.626931.3052
2327.614615.5378-8.578240.5547-31.263424.63911.4303-1.0148-2.1457-1.6874-0.00021.35061.6868-0.1501-1.431.0613-0.03510.17070.2920.14091.134543.7097-25.581822.843
240.8979-0.1151-0.29990.6366-0.00251.2122-0.0428-0.036-0.07820.11940.0111-0.0140.06380.07660.03180.02990.0098-0.01260.0389-0.00380.043850.6394-6.810624.0747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 4
2X-RAY DIFFRACTION2A5 - 91
3X-RAY DIFFRACTION3A92 - 189
4X-RAY DIFFRACTION4A190 - 205
5X-RAY DIFFRACTION5A206 - 238
6X-RAY DIFFRACTION6A239 - 253
7X-RAY DIFFRACTION7B0 - 4
8X-RAY DIFFRACTION8B5 - 90
9X-RAY DIFFRACTION9B91 - 180
10X-RAY DIFFRACTION10B181 - 194
11X-RAY DIFFRACTION11B200 - 208
12X-RAY DIFFRACTION12B209 - 253
13X-RAY DIFFRACTION13C0 - 4
14X-RAY DIFFRACTION14C5 - 90
15X-RAY DIFFRACTION15C91 - 161
16X-RAY DIFFRACTION16C162 - 207
17X-RAY DIFFRACTION17C208 - 240
18X-RAY DIFFRACTION18C241 - 253
19X-RAY DIFFRACTION19D-1 - 4
20X-RAY DIFFRACTION20D5 - 90
21X-RAY DIFFRACTION21D91 - 163
22X-RAY DIFFRACTION22D164 - 201
23X-RAY DIFFRACTION23D202 - 209
24X-RAY DIFFRACTION24D210 - 253

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