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- PDB-5yrv: Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared ... -

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Basic information

Entry
Database: PDB / ID: 5yrv
TitleDiol dehydratase, AdoCbl/1,2-propanediol, 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 / : / 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: 1.55 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)398,42047
Polymers390,96712
Non-polymers7,45335
Water59,4313299
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)199,24824
Polymers195,4846
Non-polymers3,76518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34390 Å2
ΔGint-234 kcal/mol
Surface area49620 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)199,17223
Polymers195,4846
Non-polymers3,68917
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34380 Å2
ΔGint-238 kcal/mol
Surface area49700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.777, 95.666, 114.514
Angle α, β, γ (deg.)80.61, 87.77, 81.25
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 , 7 types, 3334 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 / Propanediol


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


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


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


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


Mass: 18.015 Da / Num. of mol.: 3299 / 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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→44 Å / Num. obs: 817733 / % possible obs: 93.7 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.049 / Net I/σ(I): 13.32
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 58178 / CC1/2: 0.639 / Rrim(I) all: 0.721 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IWB

1iwb


Resolution: 1.55→44 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.69
Details: The structure factor file contains friedel pairs in F_PLUS/MINUS and I_PLUS/MINUS columns.
RfactorNum. reflection% reflection
Rfree0.1813 8339 1.02 %
Rwork0.1552 --
obs0.1555 817701 93.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26668 0 475 3299 30442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00627863
X-RAY DIFFRACTIONf_angle_d1.08837936
X-RAY DIFFRACTIONf_dihedral_angle_d13.32617183
X-RAY DIFFRACTIONf_chiral_restr0.0554285
X-RAY DIFFRACTIONf_plane_restr0.0065010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5508-1.56840.31852540.300724571X-RAY DIFFRACTION85
1.5684-1.58690.27072800.261926888X-RAY DIFFRACTION93
1.5869-1.60630.26052780.253126712X-RAY DIFFRACTION93
1.6063-1.62660.28152790.242426858X-RAY DIFFRACTION93
1.6266-1.6480.25822800.240626998X-RAY DIFFRACTION93
1.648-1.67060.26352720.231526810X-RAY DIFFRACTION94
1.6706-1.69440.27612800.224827111X-RAY DIFFRACTION94
1.6944-1.71970.25082770.218526900X-RAY DIFFRACTION94
1.7197-1.74660.22932740.218427140X-RAY DIFFRACTION94
1.7466-1.77520.24943020.210927209X-RAY DIFFRACTION94
1.7752-1.80580.24792470.206626998X-RAY DIFFRACTION94
1.8058-1.83870.2572900.197527058X-RAY DIFFRACTION94
1.8387-1.87410.20882740.189827305X-RAY DIFFRACTION94
1.8741-1.91230.21482820.183827174X-RAY DIFFRACTION94
1.9123-1.95390.2142840.175427055X-RAY DIFFRACTION94
1.9539-1.99930.19462810.174127090X-RAY DIFFRACTION94
1.9993-2.04930.20122800.174127156X-RAY DIFFRACTION94
2.0493-2.10480.19622740.163527128X-RAY DIFFRACTION94
2.1048-2.16670.16212900.152826985X-RAY DIFFRACTION94
2.1667-2.23660.16612710.146727092X-RAY DIFFRACTION94
2.2366-2.31660.17292720.146626953X-RAY DIFFRACTION94
2.3166-2.40930.18052870.151226992X-RAY DIFFRACTION94
2.4093-2.51890.1812720.150927045X-RAY DIFFRACTION93
2.5189-2.65170.17922770.151526778X-RAY DIFFRACTION93
2.6517-2.81790.16962720.151726815X-RAY DIFFRACTION93
2.8179-3.03540.20212830.153327012X-RAY DIFFRACTION94
3.0354-3.34080.16972810.144826950X-RAY DIFFRACTION94
3.3408-3.8240.16472720.128127199X-RAY DIFFRACTION94
3.824-4.8170.11892860.109527674X-RAY DIFFRACTION96
4.817-45.80610.14152880.121327706X-RAY DIFFRACTION96
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)
10.7535-0.04270.15180.3317-0.17140.3990.06730.0218-0.1371-0.0398-0.0602-0.01240.05520.02880.00140.11090.0159-0.01660.1008-0.01780.1276-94.7377158.5959-26.9011
20.8860.0998-0.07860.9865-0.17210.96440.0336-0.0643-0.37690.0249-0.01180.12880.1491-0.1334-0.01910.1344-0.015-0.04140.14780.0090.3108-118.2372142.0657-18.0643
31.5305-0.1286-0.3190.5051-0.1791.00790.0459-0.2203-0.37210.0071-0.0517-0.05520.15270.08540.01450.15370.0016-0.05660.20160.06250.2495-81.6654146.5485-10.3195
40.6065-0.030.20270.3131-0.13160.60870.00210.1080.14430.0272-0.03330.0046-0.1201-0.00850.03230.15950.03890.00660.11970.00590.1468-105.9746191.3768-45.6826
50.74280.2554-0.04070.9280.22171.6514-0.03770.49260.1029-0.23430.094-0.0153-0.02590.1658-0.05030.21430.03330.00610.42770.05050.1842-107.6962187.3372-75.3919
60.64020.07780.180.4918-0.11510.801-0.05390.05410.35270.1447-0.0306-0.0253-0.3526-0.00540.0630.39640.0389-0.04420.16780.05680.3992-105.0645214.9817-50.0558
70.3152-0.20080.1080.6206-0.14120.4565-0.0118-0.01230.0682-0.0604-0.0072-0.0759-0.0141-0.0650.02170.1364-0.02780.00140.1789-0.02290.1378-137.6325199.55556.7098
81.0038-0.31520.07021.3468-0.24371.0741-0.0614-0.29840.29450.25170.0139-0.1337-0.2345-0.21930.04560.25150.0115-0.05950.3152-0.11750.2655-141.6345225.360421.8527
91.0943-0.6726-0.56681.12840.42591.06240.05870.13570.0685-0.1956-0.0407-0.0056-0.0587-0.1478-0.00910.2446-0.0142-0.03460.28740.00460.1914-151.1819209.5462-11.1099
100.3869-0.17990.09390.6691-0.10430.3341-0.0535-0.0802-0.02020.05530.05120.02240.0234-0.07470.00230.1313-0.03730.01660.1709-0.00290.1136-127.5239169.349529.8985
111.4402-0.39940.09510.9298-0.0931.0347-0.08550.00650.07180.02050.0336-0.20410.03810.14460.05290.1548-0.0440.010.2056-0.02160.1826-97.5137166.340431.6725
121.0561-0.1453-0.36370.74880.05350.7257-0.0591-0.1865-0.22680.1620.05360.20430.1665-0.08320.01840.2631-0.05680.03870.20520.07770.2199-129.2011146.456137.4237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 604)
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 604)
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 604)
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 604)
11X-RAY DIFFRACTION11(chain 'K' and resid 43 through 1601)
12X-RAY DIFFRACTION12(chain 'L' and resid 38 through 173)

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