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- PDB-12kh: The Condensation Domain from Coprococcus Eutactus, OaaC -

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Basic information

Entry
Database: PDB / ID: 12kh
TitleThe Condensation Domain from Coprococcus Eutactus, OaaC
ComponentsCondensation Domain Protein
KeywordsBIOSYNTHETIC PROTEIN / Condensation / NRPS / fatty acid / small molecule amine
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesCoprococcus eutactus ATCC 27759 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSingh, J. / Grant, T.D. / Gulick, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136235 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM133998 United States
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Structure of a Stand-Alone Homodimeric Nonribosomal Peptide Synthetase Condensation Domain Reveals Occlusion of the Canonical Carrier-Protein Interface.
Authors: Singh, J. / Grant, T.D. / Gulick, A.M.
History
DepositionApr 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Condensation Domain Protein
B: Condensation Domain Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,75824
Polymers108,6052
Non-polymers2,15222
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.550, 122.550, 233.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Condensation Domain Protein


Mass: 54302.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chain A and B of our sample sequence should map to residues 1-463 of the reference sequence, with only position 79 differing from a ARG in the reference and HIS in our sample sequence (OaaC). ...Details: Chain A and B of our sample sequence should map to residues 1-463 of the reference sequence, with only position 79 differing from a ARG in the reference and HIS in our sample sequence (OaaC). We would like to request that the NCBI accession WP_004853257.1 is placed in the deposition somewhere, so that readers may be able to located the original accurate sequence.
Source: (gene. exp.) Coprococcus eutactus ATCC 27759 (bacteria)
Gene: COEU31_04500, DWX94_12740 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BAP1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.24 Å3/Da / Density % sol: 62 % / Description: Rhombohedral
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: OaaC at 12 mg/mL and a crystallization cocktail of 0.1 M CHES, NaOH, pH 9, 3mM AVA, 35% PEG 3000 w/v, and a protein:cocktail drop volume ration of 2:1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 23, 2025 / Details: Dectris Eiger2 XE 16M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→51.75 Å / Num. obs: 10103 / % possible obs: 99.57 % / Redundancy: 6.2 % / Biso Wilson estimate: 44.88 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09688 / Rpim(I) all: 0.04176 / Rrim(I) all: 0.1056 / Net I/σ(I): 8.65
Reflection shellResolution: 2.15→2.18 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.8448 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 1830 / CC1/2: 0.777 / Rpim(I) all: 0.3916 / Rrim(I) all: 0.9336 / % possible all: 98.59

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→51.75 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 -5.07 %
Rwork0.2013 --
obs0.2032 2664 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→51.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7480 0 141 325 7946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037785
X-RAY DIFFRACTIONf_angle_d0.56310502
X-RAY DIFFRACTIONf_dihedral_angle_d15.2852939
X-RAY DIFFRACTIONf_chiral_restr0.0441122
X-RAY DIFFRACTIONf_plane_restr0.0041354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.40251450.36842519X-RAY DIFFRACTION99
2.18-2.210.38061590.34342573X-RAY DIFFRACTION99
2.21-2.240.35841420.33562580X-RAY DIFFRACTION99
2.24-2.270.33791300.31972593X-RAY DIFFRACTION99
2.27-2.310.33211410.31852572X-RAY DIFFRACTION99
2.31-2.340.32981310.29462592X-RAY DIFFRACTION99
2.34-2.380.28461390.28482615X-RAY DIFFRACTION100
2.38-2.430.33281160.28342582X-RAY DIFFRACTION100
2.43-2.470.33841340.26992613X-RAY DIFFRACTION99
2.47-2.530.31671230.2682610X-RAY DIFFRACTION100
2.53-2.580.30881730.25372564X-RAY DIFFRACTION100
2.58-2.640.32121550.24542601X-RAY DIFFRACTION100
2.64-2.710.28721350.24862630X-RAY DIFFRACTION100
2.71-2.780.32251290.24492625X-RAY DIFFRACTION100
2.78-2.860.32611280.24512597X-RAY DIFFRACTION100
2.86-2.950.32811320.23562587X-RAY DIFFRACTION100
2.95-3.060.27161540.2282624X-RAY DIFFRACTION100
3.06-3.180.30841500.21462579X-RAY DIFFRACTION100
3.18-3.330.25171610.20552588X-RAY DIFFRACTION100
3.33-3.50.21411250.19282631X-RAY DIFFRACTION100
3.5-3.720.24061230.18242584X-RAY DIFFRACTION99
3.72-4.010.18921430.15872562X-RAY DIFFRACTION100
4.01-4.410.19641210.15972638X-RAY DIFFRACTION100
4.41-5.050.16281430.14722618X-RAY DIFFRACTION100
5.05-6.360.19751220.18512611X-RAY DIFFRACTION100
6.36-51.750.18031470.15622582X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -32.2653 Å / Origin y: 17.6278 Å / Origin z: -18.2644 Å
111213212223313233
T0.2636 Å20.0476 Å20.0288 Å2-0.3179 Å2-0.019 Å2--0.5872 Å2
L0.5523 °20.0932 °2-0.1598 °2-0.462 °2-0.2238 °2--1.039 °2
S-0.0333 Å °0.0488 Å °-0.0974 Å °-0.0412 Å °-0.0242 Å °-0.1683 Å °0.091 Å °0.1243 Å °0.0611 Å °
Refinement TLS groupSelection details: all

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