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- PDB-5ysh: Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aero... -

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Basic information

Entry
Database: PDB / ID: 5ysh
TitleDiol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal
Components(Diol dehydrase ...) x 3
KeywordsLYASE / Adenosylcobalamin / Radical enzyme
Function / homology
Function and homology information


propanediol dehydratase / propanediol dehydratase activity / cobalamin binding / metal ion binding
Similarity search - Function
Propanediol/glycerol dehydratase, small subunit / Diol/glycerol dehydratase, large subunit / Hypothetical Protein Yqey; Chain: A; domain1 / Diol/glycerol dehydratase, large subunit / Propanediol/glycerol dehydratase, small subunit / Propanediol/glycerol dehydratase, medium subunit / Propanediol/glycerol dehydratase, small subunit superfamily / Diol/glycerol dehydratase, large subunit superfamily / Dehydratase large subunit / Dehydratase small subunit ...Propanediol/glycerol dehydratase, small subunit / Diol/glycerol dehydratase, large subunit / Hypothetical Protein Yqey; Chain: A; domain1 / Diol/glycerol dehydratase, large subunit / Propanediol/glycerol dehydratase, small subunit / Propanediol/glycerol dehydratase, medium subunit / Propanediol/glycerol dehydratase, small subunit superfamily / Diol/glycerol dehydratase, large subunit superfamily / Dehydratase large subunit / Dehydratase small subunit / Diol/glycerol dehydratase/dehydratase reactivating factor / Dehydratase medium subunit / B12-dependent dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Cobalamin (vitamin B12)-dependent enzyme, catalytic / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / : / S-1,2-PROPANEDIOL / Diol dehydrase alpha subunit / Diol dehydrase beta subunit / Diol dehydrase gamma subunit
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShibata, N.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Authors: Shibata, N. / Sueyoshi, Y. / Higuchi, Y. / Toraya, T.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diol dehydrase alpha subunit
B: Diol dehydrase beta subunit
C: Diol dehydrase gamma subunit
D: Diol dehydrase alpha subunit
E: Diol dehydrase beta subunit
F: Diol dehydrase gamma subunit
G: Diol dehydrase alpha subunit
H: Diol dehydrase beta subunit
I: Diol dehydrase gamma subunit
J: Diol dehydrase alpha subunit
K: Diol dehydrase beta subunit
L: Diol dehydrase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,95136
Polymers390,84712
Non-polymers7,10424
Water23,4201300
1
A: Diol dehydrase alpha subunit
B: Diol dehydrase beta subunit
C: Diol dehydrase gamma subunit
D: Diol dehydrase alpha subunit
E: Diol dehydrase beta subunit
F: Diol dehydrase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,97518
Polymers195,4236
Non-polymers3,55212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32890 Å2
ΔGint-149 kcal/mol
Surface area49960 Å2
MethodPISA
2
G: Diol dehydrase alpha subunit
H: Diol dehydrase beta subunit
I: Diol dehydrase gamma subunit
J: Diol dehydrase alpha subunit
K: Diol dehydrase beta subunit
L: Diol dehydrase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,97518
Polymers195,4236
Non-polymers3,55212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32740 Å2
ΔGint-144 kcal/mol
Surface area50220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.330, 110.490, 115.480
Angle α, β, γ (deg.)92.69, 95.97, 105.44
Int Tables number1
Space group name H-MP1

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Components

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Diol dehydrase ... , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Diol dehydrase alpha subunit / Propanediol dehydratase / Propanediol dehydratase large subunit


Mass: 60378.102 Da / Num. of mol.: 4 / Mutation: T172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: pddA, pduC, AB185_12495, SAMEA2273575_05741 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q59470, propanediol dehydratase
#2: Protein
Diol dehydrase beta subunit


Mass: 21721.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: pddB / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q59471, propanediol dehydratase
#3: Protein
Diol dehydrase gamma subunit / Propanediol dehydratase / Propanediol dehydratase small subunit


Mass: 15611.735 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria)
Gene: pddC, pduE, pduE_1, AB185_12485, SAMEA2273639_01293, SAMEA2273697_01477
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q59472, propanediol dehydratase

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Non-polymers , 6 types, 1324 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3
#8: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1300 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 10.7% (w/v) PEG 3000, 8.6% (w/v) PEG 2000 MME, 50mM Tris pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49 Å / Num. obs: 260267 / % possible obs: 98.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.116 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 18289 / CC1/2: 0.721 / Rrim(I) all: 0.963 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IWB

1iwb


Resolution: 1.9→49 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.8
RfactorNum. reflection% reflection
Rfree0.1914 2000 0.77 %
Rwork0.1635 --
obs0.1637 260238 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26480 0 440 1300 28220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727516
X-RAY DIFFRACTIONf_angle_d1.08537407
X-RAY DIFFRACTIONf_dihedral_angle_d14.2316908
X-RAY DIFFRACTIONf_chiral_restr0.0574215
X-RAY DIFFRACTIONf_plane_restr0.0064931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.896-1.94340.31861350.271517435X-RAY DIFFRACTION93
1.9434-1.99590.25371440.225818528X-RAY DIFFRACTION99
1.9959-2.05460.24861430.204418582X-RAY DIFFRACTION99
2.0546-2.1210.23561440.19718507X-RAY DIFFRACTION99
2.121-2.19680.20991430.185918521X-RAY DIFFRACTION99
2.1968-2.28470.2251420.182218313X-RAY DIFFRACTION98
2.2847-2.38870.21591450.173918597X-RAY DIFFRACTION100
2.3887-2.51460.20571440.168118661X-RAY DIFFRACTION99
2.5146-2.67220.19281430.167718456X-RAY DIFFRACTION99
2.6722-2.87850.23451420.16918365X-RAY DIFFRACTION98
2.8785-3.16810.19931440.173818648X-RAY DIFFRACTION100
3.1681-3.62640.18481440.161118582X-RAY DIFFRACTION99
3.6264-4.56840.14251430.130418486X-RAY DIFFRACTION99
4.5684-48.93190.1561440.135718557X-RAY DIFFRACTION99
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)
11.39840.8778-0.10461.9291-0.28120.69760.0501-0.1622-0.30960.0597-0.08670.11250.2524-0.01510.00610.15620.0260.00630.14830.01510.2536105.2368127.0017-87.2414
20.4117-0.09310.03610.5991-0.00640.18520.1490.0195-1.12380.0246-0.0823-0.62170.58750.29830.00930.44810.4496-0.05950.09530.21431.7268123.3028102.8256-89.3709
30.61220.14170.27091.23920.10340.95220.0091-0.197-0.40590.01260.16470.3710.5325-0.41730.08510.3619-0.1467-0.02010.1716-0.01920.814886.7874111.4699-90.4178
41.19361.0287-0.23061.8338-0.26780.58050.0591-0.12140.12220.0439-0.07060.0955-0.06510.06-0.01120.03360.0639-0.00730.1508-0.0270.1203123.9998161.2128-93.7581
50.65210.32970.45640.76580.01630.42070.0164-0.22910.36010.925-0.3503-0.2816-0.55750.34390.1150.7817-0.3089-0.28730.5572-0.03880.2488134.9382173.112-68.3756
61.35130.2323-0.08871.68810.07321.20320.07490.11070.5608-0.12130.0030.1676-0.29340.0354-0.07490.2364-0.01270.0130.13790.02970.3312125.7264183.3016-103.5603
70.99690.48820.13191.74050.11191.2232-0.13080.1981-0.16-0.09890.1037-0.14840.26690.17220.0290.4277-0.0120.03870.3179-0.02630.1298101.2414163.3663-144.9633
80.69210.5340.61371.17570.91341.7076-0.09340.2359-0.1569-0.51670.07890.35070.894-0.1712-0.02191.1423-0.3601-0.19690.498-0.0920.209181.7181153.4904-166.3837
92.1610.71490.42151.9730.06191.1740.0195-0.0107-0.6580.35120.0224-0.34180.80470.1284-0.02870.95270.06380.03030.3026-0.0110.3912101.118140.9825-135.67
100.90260.1599-0.24911.4376-0.20771.1428-0.02870.11370.35270.08260.0030.1252-0.60830.15980.03390.6835-0.1083-0.08920.29760.05820.296499.7277202.7605-142.0311
110.92270.352-0.45960.5536-0.12460.23780.11440.19860.4663-0.1666-0.1465-0.301-0.94960.67430.05011.6839-0.7054-0.02961.02150.28840.6445121.4118215.5539-158.7018
121.19730.5930.03641.57130.27140.6834-0.1165-0.10610.60870.2740.01170.286-0.7906-0.02180.07511.4242-0.0984-0.03190.3975-0.03630.700398.2196223.5259-129.4864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 551)
2X-RAY DIFFRACTION2(chain 'B' and resid 46 through 1601)
3X-RAY DIFFRACTION3(chain 'C' and resid 38 through 173)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 550)
5X-RAY DIFFRACTION5(chain 'E' and resid 47 through 1601)
6X-RAY DIFFRACTION6(chain 'F' and resid 38 through 173)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 550)
8X-RAY DIFFRACTION8(chain 'H' and resid 44 through 1601)
9X-RAY DIFFRACTION9(chain 'I' and resid 38 through 173)
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 551)
11X-RAY DIFFRACTION11(chain 'K' and resid 49 through 1601)
12X-RAY DIFFRACTION12(chain 'L' and resid 38 through 173)

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