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- PDB-9lnf: Crystal structure of SpoIVB_101-426-S378A -

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Basic information

Entry
Database: PDB / ID: 9lnf
TitleCrystal structure of SpoIVB_101-426-S378A
ComponentsSpoIVB peptidase 42 kDa isoform
KeywordsHYDROLASE / SpoIVB / Sporulation
Function / homology
Function and homology information


SpoIVB peptidase / sporulation resulting in formation of a cellular spore / serine-type peptidase activity / proteolysis
Similarity search - Function
Peptidase S55, SpoIVB / Peptidase S55, sporulation stage IV, protein B / SpoIVB peptidase S55 / SpoIVB peptidase domain profile. / PDZ domain 6 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsJiang, L.G. / Zhu, J. / Huang, M.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370990 China
CitationJournal: To Be Published
Title: Crystal structure of SpoIVB_101-426-S378A
Authors: Jiang, L.G. / Zhu, J. / Huang, M.D.
History
DepositionJan 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 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: SpoIVB peptidase 42 kDa isoform


Theoretical massNumber of molelcules
Total (without water)35,5791
Polymers35,5791
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.190, 72.190, 108.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein SpoIVB peptidase 42 kDa isoform / Sporulation factor IV B protease


Mass: 35578.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: spoIVB, BSU24230 / Production host: Escherichia coli (E. coli) / References: UniProt: P17896
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.2 M lithium sulfate, and 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 11228 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Net I/σ(I): 32.8
Reflection shellResolution: 2.49→2.59 Å / Num. unique obs: 1143 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→23.63 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2874 544 4.87 %
Rwork0.2356 --
obs0.2379 11172 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 0 12 2509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012538
X-RAY DIFFRACTIONf_angle_d1.2843418
X-RAY DIFFRACTIONf_dihedral_angle_d7.399343
X-RAY DIFFRACTIONf_chiral_restr0.069390
X-RAY DIFFRACTIONf_plane_restr0.01441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.740.34511540.34212617X-RAY DIFFRACTION100
2.74-3.140.36291320.27762673X-RAY DIFFRACTION100
3.14-3.950.29961320.26772644X-RAY DIFFRACTION100
3.95-23.630.25121260.19612694X-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)
10.5737-0.1646-0.13090.02290.04960.89950.1052-0.1553-0.10020.15910.0988-0.20971.51640.66820.0030.6355-0.1567-0.17670.3979-0.0450.532215.51212.28966.554
20.15030.08460.01470.0404-0.02130.0422-0.4769-0.46180.12430.58750.9121-0.96950.7910.84260.0041.34390.3174-0.31851.53330.01170.98926.20518.89498.394
30.08880.03910.00870.0629-0.04370.054-0.68190.38520.4238-0.1513-0.0056-1.25290.02340.21580.00481.01460.07970.01191.6657-0.24781.289433.39419.01489.71
41.3039-0.53110.32650.6287-0.15021.1388-0.2502-0.5169-0.0296-0.19960.2606-0.07130.5631-0.1587-0.01190.6421-0.0993-0.03650.58420.05470.537513.57716.85582.81
50.16650.0093-0.07040.1231-0.19680.64970.4237-0.37290.0945-0.1581-0.19230.37280.0238-0.04810.00091.1493-0.2579-0.04090.65760.01620.74621.09714.7978.29
61.1901-0.3538-0.37981.493-0.25991.93560.15170.08640.0166-0.03590.0374-0.14280.2842-0.64340.00370.5646-0.1931-0.10340.47080.04410.42934.25119.72161.134
70.0169-0.18510.13840.502-0.74771.16660.16080.0638-0.25340.17930.1166-0.18940.66260.17250.00030.67150.0281-0.07790.3907-0.0560.555414.3119.07760.097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -4:127 )A-4 - 127
2X-RAY DIFFRACTION2( CHAIN A AND RESID 128:175 )A128 - 175
3X-RAY DIFFRACTION3( CHAIN A AND RESID 176:191 )A176 - 191
4X-RAY DIFFRACTION4( CHAIN A AND RESID 192:264 )A192 - 264
5X-RAY DIFFRACTION5( CHAIN A AND RESID 265:288 )A265 - 288
6X-RAY DIFFRACTION6( CHAIN A AND RESID 289:395 )A289 - 395
7X-RAY DIFFRACTION7( CHAIN A AND RESID 396:426 )A396 - 426

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