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- PDB-7mgo: Crystal structure of F501H variant of 2-ketopropyl coenzyme M oxi... -

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Basic information

Entry
Database: PDB / ID: 7mgo
TitleCrystal structure of F501H variant of 2-ketopropyl coenzyme M oxidoreductase/carboxylase (2-KPCC) from Xanthobacter autotrophicus
Components2-oxopropyl-CoM reductase, carboxylating
KeywordsOXIDOREDUCTASE / carboxylation / oxidation-reduction / carbon dioxide fixation / carbon-carbon bond / anion-binding / kinetics
Function / homology
Function and homology information


2-oxopropyl-CoM reductase (carboxylating) / 2-oxopropyl-CoM reductase (carboxylating) activity / propylene catabolic process
Similarity search - Function
Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1-THIOETHANESULFONIC ACID / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / 2-oxopropyl-CoM reductase, carboxylating
Similarity search - Component
Biological speciesXanthobacter autotrophicus Py2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPrussia, G. / Zadvornyy, O.A. / Peters, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0018143 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: The unique Phe-His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S-C bond cleavage.
Authors: Prussia, G.A. / Shisler, K.A. / Zadvornyy, O.A. / Streit, B.R. / DuBois, J.L. / Peters, J.W.
History
DepositionApr 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-oxopropyl-CoM reductase, carboxylating
B: 2-oxopropyl-CoM reductase, carboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7198
Polymers114,8112
Non-polymers1,9086
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-96 kcal/mol
Surface area33930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.093, 60.209, 104.978
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2-oxopropyl-CoM reductase, carboxylating / Aliphatic epoxide carboxylation component II / NADPH:2-ketopropyl-CoM carboxylase/oxidoreductase / 2-KPCC


Mass: 57405.316 Da / Num. of mol.: 2 / Mutation: F501H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus Py2 (bacteria)
Strain: ATCC BAA-1158 / Py2 / Gene: xecC, Xaut_4867
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q56839, 2-oxopropyl-CoM reductase (carboxylating)
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.17 M ammonium acetate, 0.085 M trisodium citrate pH 5.6, 27% PEG 4,000, and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9884 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9884 Å / Relative weight: 1
ReflectionResolution: 1.85→39.19 Å / Num. obs: 87767 / % possible obs: 95.9 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.066 / Net I/σ(I): 13.2
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.705 / Num. unique obs: 10655 / CC1/2: 0.685 / Rpim(I) all: 0.461 / Rrim(I) all: 0.848

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c3c

2c3c


Resolution: 1.85→39.19 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 4351 4.96 %
Rwork0.1716 --
obs0.1731 87717 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7870 0 16 667 8553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138070
X-RAY DIFFRACTIONf_angle_d1.26410932
X-RAY DIFFRACTIONf_dihedral_angle_d12.3441126
X-RAY DIFFRACTIONf_chiral_restr0.0831196
X-RAY DIFFRACTIONf_plane_restr0.0091413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.36381220.31292051X-RAY DIFFRACTION71
1.87-1.890.27121090.2972236X-RAY DIFFRACTION77
1.89-1.920.39441310.28382273X-RAY DIFFRACTION80
1.92-1.940.31371210.26822551X-RAY DIFFRACTION87
1.94-1.970.26481610.23842593X-RAY DIFFRACTION92
1.97-1.990.22391420.23342871X-RAY DIFFRACTION99
1.99-2.020.25471580.21162879X-RAY DIFFRACTION99
2.02-2.050.23761300.21122850X-RAY DIFFRACTION99
2.05-2.080.26431600.2052893X-RAY DIFFRACTION99
2.08-2.120.23421370.2062839X-RAY DIFFRACTION99
2.12-2.150.25641460.19732867X-RAY DIFFRACTION99
2.15-2.190.22791430.19742819X-RAY DIFFRACTION98
2.19-2.240.23641700.19712808X-RAY DIFFRACTION97
2.24-2.280.22011550.19672772X-RAY DIFFRACTION96
2.28-2.330.22831440.17922870X-RAY DIFFRACTION99
2.33-2.380.22151450.18342851X-RAY DIFFRACTION99
2.39-2.440.21041660.18072821X-RAY DIFFRACTION99
2.44-2.510.19351510.17642935X-RAY DIFFRACTION99
2.51-2.580.19111600.1672787X-RAY DIFFRACTION98
2.58-2.670.23621500.18312843X-RAY DIFFRACTION98
2.67-2.760.1961440.18152828X-RAY DIFFRACTION97
2.76-2.870.21161100.18222922X-RAY DIFFRACTION99
2.87-30.1941560.18012866X-RAY DIFFRACTION99
3-3.160.22271490.172889X-RAY DIFFRACTION99
3.16-3.360.18651600.16242882X-RAY DIFFRACTION99
3.36-3.620.20611400.15382841X-RAY DIFFRACTION97
3.62-3.980.18841480.13452902X-RAY DIFFRACTION99
3.98-4.560.13191460.13022938X-RAY DIFFRACTION100
4.56-5.740.17031500.14312897X-RAY DIFFRACTION98
5.74-39.190.19221470.17482992X-RAY DIFFRACTION98
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)
10.6363-0.0768-0.09640.91830.18430.89860.14110.59190.0399-0.9702-0.38640.5968-0.1611-0.37520.14860.68360.0697-0.25490.6523-0.07360.5072-8.02-3.268111.037
21.3114-0.3995-0.39270.88570.15740.5572-0.02850.2068-0.0615-0.2053-0.03480.29850.0499-0.20460.08060.2079-0.0367-0.06040.2647-0.00160.252-5.0456.527136.802
31.0391-0.1774-0.20040.79720.1220.6825-0.06670.0182-0.1713-0.12250.04780.02130.0936-0.06450.01520.2233-0.03980.00230.2149-0.00610.188315.926-6.088138.242
40.8366-0.07480.19870.6032-0.16760.3957-0.0227-0.09110.03950.0060.061-0.2047-0.11850.0875-0.0290.2409-0.04780.02570.2605-0.06720.312440.0059.821144.413
50.57670.04260.02340.4773-0.1310.4201-0.01260.09080.0951-0.26880.0698-0.2059-0.1560.0918-0.03740.4046-0.09650.10270.2512-0.03430.290737.84521.414121.182
61.0851-0.15810.26170.5987-0.20460.44710.01940.1524-0.1065-0.22180.0544-0.2452-0.01150.1433-0.07780.3085-0.05030.08770.2715-0.07540.316140.788-2.122128.809
70.79-0.0311-0.28091.319-0.08810.6912-0.02430.2094-0.1262-0.44710.04750.12670.0876-0.1171-0.01640.4056-0.0733-0.02870.3039-0.03040.196114.862-1.082117.716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:73 )A4 - 73
2X-RAY DIFFRACTION2( CHAIN A AND RESID 74:337 )A74 - 337
3X-RAY DIFFRACTION3( CHAIN A AND RESID 338:523 )A338 - 523
4X-RAY DIFFRACTION4( CHAIN B AND RESID 3:180 )B3 - 180
5X-RAY DIFFRACTION5( CHAIN B AND RESID 181:335 )B181 - 335
6X-RAY DIFFRACTION6( CHAIN B AND RESID 336:401 )B336 - 401
7X-RAY DIFFRACTION7( CHAIN B AND RESID 402:522 )B402 - 522

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