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- PDB-9t8a: Crystal Structure of a de novo CO2 reductase A4 -

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Basic information

Entry
Database: PDB / ID: 9t8a
TitleCrystal Structure of a de novo CO2 reductase A4
ComponentsA4 CO2 reductase protein
KeywordsOXIDOREDUCTASE / de novo CO2 reductase
Function / homologyPROTOPORPHYRIN IX CONTAINING CO / DI(HYDROXYETHYL)ETHER / Chem-PG6 / TRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLevy, C.W. / Ortmayer, M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/V056565/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/V056565/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/W522065/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: A De Novo CO 2 Reductase Featuring a Cysteine-Ligated Cobalt Porphyrin Cofactor.
Authors: Radley, E.J. / Andrews, A.C. / Kalvet, I. / Deng, Y. / Bell, E.L. / Levy, C.W. / Ortmayer, M. / Heyes, D.J. / Megarity, C.F. / Nunez-Franco, R. / Hutton, A.E. / Lu, Y. / Baker, D. / Green, A.P.
History
DepositionNov 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A4 CO2 reductase protein
B: A4 CO2 reductase protein
C: A4 CO2 reductase protein
D: A4 CO2 reductase protein
E: A4 CO2 reductase protein
F: A4 CO2 reductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,60621
Polymers111,1896
Non-polymers5,41715
Water6,017334
1
A: A4 CO2 reductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4954
Polymers18,5311
Non-polymers9643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: A4 CO2 reductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4954
Polymers18,5311
Non-polymers9643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: A4 CO2 reductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4173
Polymers18,5311
Non-polymers8862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: A4 CO2 reductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3634
Polymers18,5311
Non-polymers8323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: A4 CO2 reductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4173
Polymers18,5311
Non-polymers8862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: A4 CO2 reductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4173
Polymers18,5311
Non-polymers8862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.212, 161.742, 74.587
Angle α, β, γ (deg.)90.000, 105.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
A4 CO2 reductase protein


Mass: 18531.420 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 349 molecules

#2: Chemical
ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C34H32CoN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O6
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Phosphate/Citrate 5.5 20 % v/v PEG Smear High

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.08→71.8 Å / Num. obs: 67786 / % possible obs: 99.92 % / Redundancy: 7 % / Biso Wilson estimate: 34.83 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.057 / Net I/σ(I): 7.4
Reflection shellResolution: 2.08→2.14 Å / Mean I/σ(I) obs: 0.62 / Num. unique obs: 5158 / CC1/2: 0.559 / CC star: 0.847 / Rpim(I) all: 0.618 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→71.8 Å / SU ML: 0.2747 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.91
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 1782 2.96 %
Rwork0.1983 58492 -
obs0.1994 60274 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.15 Å2
Refinement stepCycle: LAST / Resolution: 2.08→71.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7270 0 372 334 7976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197762
X-RAY DIFFRACTIONf_angle_d0.473510459
X-RAY DIFFRACTIONf_chiral_restr0.03571173
X-RAY DIFFRACTIONf_plane_restr0.00361278
X-RAY DIFFRACTIONf_dihedral_angle_d10.81263133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.36191200.30994489X-RAY DIFFRACTION99.85
2.14-2.20.28751350.26694513X-RAY DIFFRACTION99.89
2.2-2.270.3181120.24744455X-RAY DIFFRACTION99.85
2.27-2.350.24471430.22484540X-RAY DIFFRACTION99.87
2.35-2.450.27231310.21894486X-RAY DIFFRACTION99.94
2.45-2.560.26821370.22044481X-RAY DIFFRACTION99.96
2.56-2.690.27131500.21884461X-RAY DIFFRACTION99.98
2.69-2.860.25441280.20914492X-RAY DIFFRACTION99.96
2.86-3.080.24911300.21274532X-RAY DIFFRACTION100
3.08-3.390.2481250.22014532X-RAY DIFFRACTION100
3.39-3.880.20591410.18014486X-RAY DIFFRACTION100
3.88-4.890.19221510.15434524X-RAY DIFFRACTION100
4.89-71.80.2121790.17514501X-RAY DIFFRACTION99.77
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)
11.07281708852-0.860323981183-0.5087576466611.874876008180.02133656382192.94516591701-0.06552807977560.0859630122863-0.0376952455898-0.01589957950610.0565308149360.05453793192190.14276552465-0.2481484290640.003218883826580.278584892234-0.0540895071158-0.007952639610180.296694526959-0.008354583460990.205448279337-5.225079334311.1061389686528.954133486
22.36874647004-0.661555220609-0.02674883878841.76141520529-0.3161669374651.394425245230.03151124934920.162517806364-0.16486838105-0.0760234064105-0.01373830969570.001493064189170.0571117288409-0.0180625192947-0.01674574814330.249520854764-0.0313816617201-0.001288405197420.187145681109-0.002302134202790.25457085825-3.179736638429.54231699717.69138504377
30.985789843333-0.3290029898460.1792363705241.73506001732-0.4921924953933.068492497050.05411433584840.03459046189310.02536704818250.00466956186089-0.08348575316780.00365270748437-0.191636972520.1610274189960.03426452196450.254204347249-0.03671799636440.01834136523020.255396944876-0.002829325636120.229210109586-2.97080866228-4.38966060567-9.24386108319
41.586155866920.229557647777-0.2566930248152.66526641393-1.22624198433.85404863382-0.0206264442723-0.08135107641190.2968819481040.3448607832430.08614784956160.0801319968189-0.5472900215610.0679249717957-0.03005856283340.3798279345260.038117871910.01545849765590.272700357814-0.01863593819570.26776369219114.432975425820.7453184477-22.4844408192
51.801932263431.28084157573-0.09080199953561.93523790767-0.739623373962.940023805750.0522742181479-0.1698315618810.1921657718080.630637896706-0.02912888836880.262665554148-0.382451775006-0.2125936099590.003128999600130.5465762422540.05531814922840.06795669806070.2555105926810.001660294266520.325525491622-7.8688345297148.474064097128.2042458012
62.46428191366-0.861897013692-0.1081457363622.41658782463-0.4040779759461.605659515760.07335661596110.166048645836-0.262175295276-0.203833253065-0.004787802361460.1229301664930.108137788969-0.0238430984004-0.07151136686650.267408263649-0.0156392125479-0.01688268422290.210200820711-0.02888627559370.19368179711512.12940825756.3856850747-8.43919020307
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 156 / Label seq-ID: 1 - 156

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 1 through 156)AA
22(chain 'B' and resid 1 through 156)BD
33(chain 'C' and resid 1 through 156)CG
44(chain 'D' and resid 1 through 156)DJ
55(chain 'E' and resid 1 through 156)EN
66(chain 'F' and resid 1 through 156)FQ

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