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- PDB-9r4h: Spitrobot-2 advances time-resolvedcryo-trapping crystallography t... -

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Basic information

Entry
Database: PDB / ID: 9r4h
TitleSpitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: T4 Lysozyme, mutant L99A bound with indole (10 s soaking)
ComponentsEndolysin
KeywordsHYDROLASE / T4 lysozyme / L99A
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsSpiliopoulou, M. / Hatton, C.E. / Mehrabi, P. / Schulz, E.C.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)European Union
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Education and Research01KI2114 Germany
CitationJournal: Commun Chem / Year: 2025
Title: Spitrobot-2 advances time-resolved cryo-trapping crystallography to under 25 ms.
Authors: Spiliopoulou, M. / Hatton, C.E. / Kollewe, M. / Leimkohl, J.P. / Schikora, H. / Tellkamp, F. / Mehrabi, P. / Schulz, E.C.
History
DepositionMay 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6465
Polymers18,4601
Non-polymers1864
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-31 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.241, 60.241, 97.706
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 18460.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T4 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7S9SVX7, lysozyme
#2: Chemical ChemComp-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: 4 M sodium/potassium phosphate pH 7.0, 0.1 M 1,6-hexanediol, 0.15 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.493→52.17 Å / Num. obs: 31276 / % possible obs: 95.1 % / Redundancy: 18.91 % / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 1.493→1.56 Å / Num. unique obs: 1548 / CC1/2: 0.516

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Processing

Software
NameVersionClassification
XDSdata reduction
autoPROCdata reduction
Aimlessdata scaling
autoPROCdata scaling
PHASERphasing
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→52.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.413 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21586 1518 4.9 %RANDOM
Rwork0.18931 ---
obs0.19061 29757 91.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å2-0 Å2
2---0.1 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.49→52.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 12 113 1420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121335
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161305
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.8281801
X-RAY DIFFRACTIONr_angle_other_deg0.6471.7922979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3885166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.283513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.38810245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6711.962655
X-RAY DIFFRACTIONr_mcbond_other1.671.968656
X-RAY DIFFRACTIONr_mcangle_it2.3743.52818
X-RAY DIFFRACTIONr_mcangle_other2.3723.527819
X-RAY DIFFRACTIONr_scbond_it3.012.311680
X-RAY DIFFRACTIONr_scbond_other3.012.311680
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5844.085982
X-RAY DIFFRACTIONr_long_range_B_refined5.38119.71561
X-RAY DIFFRACTIONr_long_range_B_other5.35919.461543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.493→1.531 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 29 -
Rwork0.276 453 -
obs--19.51 %

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