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- PDB-9t8b: Crystal structure de novo CO2 reductase A4H73A -

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Basic information

Entry
Database: PDB / ID: 9t8b
TitleCrystal structure de novo CO2 reductase A4H73A
Componentsde novo CO2 reductase
KeywordsOXIDOREDUCTASE / De novo CO2 reductase
Function / homologyPROTOPORPHYRIN IX CONTAINING CO / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsLevy, C.W. / Ortmayer, M.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/V056565/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/V005049/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/W522065/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/RKLPMIN/I 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

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Assembly

Deposited unit
A: de novo CO2 reductase
B: de novo CO2 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,02510
Polymers36,9292
Non-polymers2,0968
Water1,40578
1
A: de novo CO2 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4905
Polymers18,4641
Non-polymers1,0264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: de novo CO2 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5345
Polymers18,4641
Non-polymers1,0704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.101, 63.427, 51.477
Angle α, β, γ (deg.)90.00, 88.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein de novo CO2 reductase


Mass: 18464.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 86 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 26 % w/v PEG 2000 MME, 0.1 M Bis-Tris pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.81→45.09 Å / Num. obs: 26502 / % possible obs: 99.89 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rpim(I) all: 0.0203 / Net I/σ(I): 18.74
Reflection shellResolution: 1.81→1.88 Å / Mean I/σ(I) obs: 2.25 / Num. unique obs: 2454 / CC1/2: 0.882 / Rpim(I) all: 0.2366

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→45.09 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1307 4.93 %
Rwork0.1976 --
obs0.1991 26502 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 143 78 2650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052598
X-RAY DIFFRACTIONf_angle_d0.743490
X-RAY DIFFRACTIONf_dihedral_angle_d25.5141059
X-RAY DIFFRACTIONf_chiral_restr0.039392
X-RAY DIFFRACTIONf_plane_restr0.007424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.880.38031460.34762750X-RAY DIFFRACTION100
1.88-1.970.29891310.26592792X-RAY DIFFRACTION100
1.97-2.070.26681470.22682777X-RAY DIFFRACTION100
2.07-2.20.25931370.21012803X-RAY DIFFRACTION100
2.2-2.370.22231270.22818X-RAY DIFFRACTION100
2.37-2.610.25151440.19222795X-RAY DIFFRACTION100
2.61-2.990.24661810.20452784X-RAY DIFFRACTION100
2.99-3.760.22661370.19722816X-RAY DIFFRACTION100
3.76-45.090.19461570.17822860X-RAY DIFFRACTION100
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)
12.8512-0.3691-0.75831.2754-0.01492.7766-0.1412-0.06460.0516-0.14360.03990.04320.07040.178-00.2853-0.0292-0.01260.21220.01440.284214.16928.2982-0.1821
21.6544-0.0843-0.40031.56160.25144.0046-0.06470.06520.0979-0.0675-0.05310.1495-0.1753-0.24490.00020.28630.006-0.00990.2952-0.00790.32187.8568-9.126-24.492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 158)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 160)

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