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- PDB-9low: Crystal structure of RamR3.0 complexed with 3-alkenynaphthoate -

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Basic information

Entry
Database: PDB / ID: 9low
TitleCrystal structure of RamR3.0 complexed with 3-alkenynaphthoate
ComponentsPutative regulatory protein
KeywordsPHOTOSYNTHESIS / photobiocatalysis / artificial photoenzyme / enantioselective synthesis
Function / homology
Function and homology information


DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
: / Putative regulatory protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, X. / Qian, J.Y. / Yang, X.J. / Wu, Y.Z. / Zhong, F.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377098 China
CitationJournal: Nat Catal / Year: 2025
Title: Enantioselective energy transfer catalysis compartmentalized by triplet photoenzymes
Authors: Yang, X.J. / Guo, J. / Qian, J.Y. / Huang, J. / Shi, J. / Jiang, M. / Zhang, J. / Pang, T. / Sun, N. / Fu, Y. / Zhao, W. / Wu, G. / Chen, X. / Wu, Y.Z. / Zhong, F.R.
History
DepositionJan 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative regulatory protein
B: Putative regulatory protein
C: Putative regulatory protein
D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,02814
Polymers93,1224
Non-polymers1,90610
Water93752
1
A: Putative regulatory protein
B: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3225
Polymers46,5612
Non-polymers7613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-35 kcal/mol
Surface area17300 Å2
MethodPISA
2
C: Putative regulatory protein
hetero molecules

D: Putative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7069
Polymers46,5612
Non-polymers1,1457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3200 Å2
ΔGint-83 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.402, 54.793, 84.885
Angle α, β, γ (deg.)98.14, 95.86, 96.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative regulatory protein


Mass: 23280.492 Da / Num. of mol.: 4 / Mutation: K63R,C67W,C134A,F155DFF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Gene: STM14_0676 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6AY66
#2: Chemical
ChemComp-A1EKZ / (phenylmethyl) 1-but-3-enoxynaphthalene-2-carboxylate / benzyl 1-(but-3-en-1-yloxy)-2-naphthoate


Mass: 332.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H20O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 0.1M MES, pH6.5, 1.6 M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→83.41 Å / Num. obs: 26685 / % possible obs: 96.7 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.084 / Rrim(I) all: 0.158 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2979 / CC1/2: 0.655 / Rrim(I) all: 0.843 / Rsym value: 0.439 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VW0

3vw0


Resolution: 2.5→28.419 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 1271 4.77 %
Rwork0.25 --
obs0.2519 26624 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→28.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 130 52 6062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076120
X-RAY DIFFRACTIONf_angle_d1.0198248
X-RAY DIFFRACTIONf_dihedral_angle_d26.7372204
X-RAY DIFFRACTIONf_chiral_restr0.074888
X-RAY DIFFRACTIONf_plane_restr0.0071044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60010.35951420.32172779X-RAY DIFFRACTION97
2.6001-2.71830.3471450.29592856X-RAY DIFFRACTION97
2.7183-2.86150.32661350.29222877X-RAY DIFFRACTION98
2.8615-3.04060.31931180.28072899X-RAY DIFFRACTION98
3.0406-3.2750.28051390.26192827X-RAY DIFFRACTION98
3.275-3.6040.30741380.25742767X-RAY DIFFRACTION96
3.604-4.12420.28691530.24112737X-RAY DIFFRACTION93
4.1242-5.19090.2561460.21072798X-RAY DIFFRACTION97
5.1909-28.4190.25011550.22122813X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 11.489 Å / Origin y: -22.0373 Å / Origin z: 18.2489 Å
111213212223313233
T0.1534 Å2-0.0181 Å20.0174 Å2-0.2165 Å2-0.0499 Å2--0.3027 Å2
L0.6032 °2-0.0035 °20.0073 °2-0.6667 °2-0.3326 °2--0.7312 °2
S-0.0571 Å °-0.0738 Å °-0.0369 Å °0.0055 Å °0.0312 Å °-0.1177 Å °-0.0202 Å °0.0216 Å °0.0389 Å °
Refinement TLS groupSelection details: all

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