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- PDB-5yrt: Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared c... -

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Basic information

Entry
Database: PDB / ID: 5yrt
TitleDiol dehydratase, AdoCbl/substrate-free, anaerobically-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 / : / 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: 1.7 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 10, 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)398,19244
Polymers390,96712
Non-polymers7,22532
Water53,1442950
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)199,09622
Polymers195,4846
Non-polymers3,61216
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33880 Å2
ΔGint-243 kcal/mol
Surface area49790 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)199,09622
Polymers195,4846
Non-polymers3,61216
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34510 Å2
ΔGint-242 kcal/mol
Surface area49630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.687, 95.459, 114.567
Angle α, β, γ (deg.)80.78, 87.58, 81.10
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: 60408.133 Da / Num. of mol.: 4
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, 2982 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-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-B12 / COBALAMIN / Vitamin B12


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


Mass: 18.015 Da / Num. of mol.: 2950 / 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: 1.98 Å3/Da / Density % sol: 37.96 %
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: BL26B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47 Å / Num. obs: 313887 / % possible obs: 94.2 % / Redundancy: 1.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.082 / Net I/σ(I): 8.33
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 24404 / CC1/2: 0.539 / Rrim(I) all: 0.917 / % possible all: 90.3

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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: 1.7→47 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.83
RfactorNum. reflection% reflection
Rfree0.1867 3094 1.02 %
Rwork0.1495 --
obs0.1498 302964 91.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26686 0 460 2950 30096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00627862
X-RAY DIFFRACTIONf_angle_d1.09637935
X-RAY DIFFRACTIONf_dihedral_angle_d13.47717184
X-RAY DIFFRACTIONf_chiral_restr0.0554282
X-RAY DIFFRACTIONf_plane_restr0.0055012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6959-1.72240.2551010.22889740X-RAY DIFFRACTION65
1.7224-1.75060.27911190.220411603X-RAY DIFFRACTION77
1.7506-1.78080.24821300.202112521X-RAY DIFFRACTION84
1.7808-1.81320.22431360.194113194X-RAY DIFFRACTION88
1.8132-1.84810.24041410.187113603X-RAY DIFFRACTION91
1.8481-1.88580.22271410.198613671X-RAY DIFFRACTION92
1.8858-1.92680.31931380.242313391X-RAY DIFFRACTION89
1.9268-1.97160.24171450.193114021X-RAY DIFFRACTION94
1.9716-2.02090.22971440.16414195X-RAY DIFFRACTION95
2.0209-2.07560.20751550.172413884X-RAY DIFFRACTION93
2.0756-2.13670.22871460.151714140X-RAY DIFFRACTION95
2.1367-2.20560.15631450.141114274X-RAY DIFFRACTION95
2.2056-2.28440.22891420.171113406X-RAY DIFFRACTION90
2.2844-2.37590.16771430.140314083X-RAY DIFFRACTION94
2.3759-2.4840.17591500.138714240X-RAY DIFFRACTION95
2.484-2.6150.17851440.136714377X-RAY DIFFRACTION96
2.615-2.77880.17341420.142613907X-RAY DIFFRACTION93
2.7788-2.99330.17841480.14314147X-RAY DIFFRACTION94
2.9933-3.29450.17251480.144614472X-RAY DIFFRACTION97
3.2945-3.7710.17111440.130114308X-RAY DIFFRACTION96
3.771-4.75030.131460.111514433X-RAY DIFFRACTION96
4.7503-46.59730.15221460.125314260X-RAY DIFFRACTION95
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)
10.4653-0.05410.07220.2601-0.12520.34230.04270.0385-0.0875-0.0277-0.04080.00460.05870.01230.00010.0890.0135-0.01090.0816-0.01290.0787-94.8412158.6449-26.9285
20.81330.20560.01331.1235-0.13431.20270.0055-0.0046-0.34210.0478-0.00430.14070.1408-0.1840.00240.0996-0.018-0.0130.1359-0.01210.2567-118.3581142.0947-18.0788
31.2334-0.0759-0.36660.5535-0.21941.22440.035-0.079-0.22940.0145-0.0532-0.04630.14160.10140.02360.11840.0179-0.03140.12390.0280.1479-81.6526146.6219-10.4855
40.4971-0.0240.14370.3086-0.11270.48810.00380.03020.12940.025-0.02230.0043-0.0795-0.03330.02160.1090.03510.00860.0960.00210.1021-106.1702191.4641-45.7296
50.94090.11220.04891.06740.14361.6291-0.03160.26920.0825-0.2340.0787-0.042-0.03590.1076-0.0430.1450.00880.00870.20130.02670.1098-107.9376187.5654-75.4889
60.7638-0.02430.07720.5344-0.22470.4614-0.0395-0.06050.35660.1434-0.0009-0.014-0.2747-0.01650.02560.28760.0414-0.03410.12890.00190.3428-105.1277215.1026-50.0295
70.2334-0.06380.01270.4231-0.06280.3295-0.00210.02230.0514-0.0295-0.0031-0.0484-0.0166-0.00790.00690.0766-0.01180.00180.0873-0.00760.0806-137.416199.44126.6924
80.7488-0.4066-0.04510.9989-0.09910.663-0.0198-0.06470.18330.11950.0166-0.1068-0.1247-0.02340.00270.1326-0.0155-0.02970.1075-0.03530.1527-141.4275225.214921.6999
91.0761-0.5677-0.71520.87470.56291.14080.05770.18180.0831-0.1657-0.04320.0111-0.0614-0.0997-0.0110.1357-0.0002-0.02370.1540.02070.0913-150.9329209.6813-11.1149
100.3102-0.03570.09350.4548-0.08050.2878-0.0195-0.0259-0.0180.05440.01010.00990.0107-0.03760.00710.0829-0.01870.01540.0799-0.00040.0746-127.5539169.57830.0179
111.0759-0.36280.08350.9055-0.00650.9798-0.03990.02170.06470.0207-0.0058-0.17740.02110.16670.03310.0898-0.03480.00450.11540.01070.1154-97.4478166.246831.6983
120.9918-0.1502-0.41560.5988-0.00860.5519-0.001-0.1573-0.19530.1392-0.01270.12510.1164-0.01280.03480.1846-0.04680.02630.1240.03410.1592-129.1339146.390437.592
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 43 through 1601)
3X-RAY DIFFRACTION3(chain 'C' and resid 38 through 173)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 551)
5X-RAY DIFFRACTION5(chain 'E' and resid 46 through 1601)
6X-RAY DIFFRACTION6(chain 'F' and resid 38 through 173)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 554)
8X-RAY DIFFRACTION8(chain 'H' and resid 46 through 1601)
9X-RAY DIFFRACTION9(chain 'I' and resid 38 through 173)
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 554)
11X-RAY DIFFRACTION11(chain 'K' and resid 43 through 1601)
12X-RAY DIFFRACTION12(chain 'L' and resid 38 through 173)

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