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- PDB-24uu: Crystal structure of Endonuclease IV from Chlamydophila pneumoniae -

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Basic information

Entry
Database: PDB / ID: 24uu
TitleCrystal structure of Endonuclease IV from Chlamydophila pneumoniae
ComponentsProbable endonuclease 4
KeywordsHYDROLASE / Endonuclease IV
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / DNA binding / zinc ion binding
Similarity search - Function
AP endonucleases family 2 signature 1. / AP endonucleases family 2 signature 2. / AP endonucleases family 2 signature 3. / AP endonuclease 2, zinc binding site / AP endonucleases family 2 profile. / AP endonuclease family 2 / AP endonuclease 2 / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / MALONATE ION / DI(HYDROXYETHYL)ETHER / PROPANOIC ACID / Probable endonuclease 4
Similarity search - Component
Biological speciesChlamydia pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsJin, J.L. / Zhang, Y.T. / Gao, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No.31070651 China
CitationJournal: Biomolecules / Year: 2026
Title: Crystal Structure and Activity Analysis of Chlamydophila pneumoniae AP Endonuclease IV.
Authors: Jin, J. / Zhang, Y. / Guo, S. / Yang, L. / Liu, H. / Liu, L. / Gao, W.
History
DepositionMar 22, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable endonuclease 4
B: Probable endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,56021
Polymers63,3782
Non-polymers1,18219
Water4,143230
1
A: Probable endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,43012
Polymers31,6891
Non-polymers74111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1309
Polymers31,6891
Non-polymers4418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.930, 68.080, 150.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable endonuclease 4 / Endodeoxyribonuclease IV / Endonuclease IV


Mass: 31688.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia pneumoniae (bacteria) / Gene: nfo, CPn_0732, CP_0014, CpB0760 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z7H3, deoxyribonuclease IV

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Non-polymers , 9 types, 249 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O2
#8: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: Precipitant: 8% v/v Tacsimate pH 5.2,25% w/v PEG 3350.Protein: 2.81 mg/mL protein, 100mmol/L NaCl, 20mmol/L Tris-HCl pH7.8. Mix the precipitant with the protein solution at a ratio of 1:1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→62.05 Å / Num. obs: 50308 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.3
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.263 / Mean I/σ(I) obs: 2 / Num. unique obs: 3474 / CC1/2: 0.749 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→31.03 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 2415 4.81 %
Rwork0.1779 --
obs-50233 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→31.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 64 230 4758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074615
X-RAY DIFFRACTIONf_angle_d0.8126237
X-RAY DIFFRACTIONf_dihedral_angle_d19.0541702
X-RAY DIFFRACTIONf_chiral_restr0.051682
X-RAY DIFFRACTIONf_plane_restr0.006815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.28421110.26872805X-RAY DIFFRACTION100
2.01-2.050.30741170.23792798X-RAY DIFFRACTION100
2.05-2.10.26211750.22062727X-RAY DIFFRACTION100
2.1-2.150.21091560.20732752X-RAY DIFFRACTION100
2.15-2.210.25241480.20112765X-RAY DIFFRACTION100
2.21-2.280.23161920.20682740X-RAY DIFFRACTION100
2.28-2.350.24681240.19712804X-RAY DIFFRACTION100
2.35-2.430.22491520.18542779X-RAY DIFFRACTION100
2.44-2.530.21921430.18752783X-RAY DIFFRACTION100
2.53-2.650.19831430.18862772X-RAY DIFFRACTION100
2.65-2.790.20991270.18972826X-RAY DIFFRACTION100
2.79-2.960.2222990.19552869X-RAY DIFFRACTION100
2.96-3.190.23531520.18952807X-RAY DIFFRACTION100
3.19-3.510.20241500.17812826X-RAY DIFFRACTION100
3.51-4.020.18691350.16112863X-RAY DIFFRACTION100
4.02-5.060.18671420.14982877X-RAY DIFFRACTION100
5.06-31.030.18611490.16393025X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.6157 Å / Origin y: -0.5616 Å / Origin z: 11.1996 Å
111213212223313233
T0.2763 Å2-0.012 Å2-0.0327 Å2-0.3194 Å20.023 Å2--0.3071 Å2
L1.4205 °2-0.1183 °20.1289 °2-1.4211 °2-0.7494 °2--1.4367 °2
S0.0505 Å °0.4218 Å °0.0417 Å °-0.1518 Å °0.0366 Å °0.0726 Å °0.2112 Å °-0.0998 Å °-0.0771 Å °
Refinement TLS groupSelection details: all

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