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- PDB-9csn: Crystal structure of human ribonuclease 7 (RNase 7) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9csn
TitleCrystal structure of human ribonuclease 7 (RNase 7) in complex with 5'-adenosine monophosphate (5'-AMP)
ComponentsRibonuclease 7
KeywordsHYDROLASE / ribonuclease / RNase 7 / transphosphorylase
Function / homology
Function and homology information


cytolysis in another organism / peptidoglycan binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Antimicrobial peptides / RNA nuclease activity / defense response to fungus / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / endonuclease activity ...cytolysis in another organism / peptidoglycan binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Antimicrobial peptides / RNA nuclease activity / defense response to fungus / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / endonuclease activity / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / innate immune response / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BORIC ACID / Ribonuclease 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsTran, T.T.Q. / Pham, N.T.H. / Calmettes, C. / Doucet, N.
Funding support Canada, 6items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04368 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)CREATE APRENTICE Canada
Fonds de Recherche du Quebec - Sante (FRQS)281993 Canada
Canada Foundation for InnovationMSI - GlycoNet Integrated Services Canada
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)PROTEO Canada
CitationJournal: To Be Published
Title: Crystal structure of human ribonuclease 7 (RNase 7) in complex with 5'-adenosine monophosphate (5'-AMP)
Authors: Tran, T.T.Q. / Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionJul 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 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: Ribonuclease 7
B: Ribonuclease 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,53916
Polymers29,3262
Non-polymers1,21314
Water1,76598
1
A: Ribonuclease 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,53610
Polymers14,6631
Non-polymers8739
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0036
Polymers14,6631
Non-polymers3405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.110, 48.170, 62.900
Angle α, β, γ (deg.)90.00, 97.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ribonuclease 7 / RNase 7 / Skin-derived antimicrobial protein 2 / SAP-2


Mass: 14663.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE7, UNQ2516/PRO6006 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9H1E1, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Non-polymers , 5 types, 112 molecules

#2: Chemical
ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: BH3O3
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M MIB (malonic acid:imidazole:boric acid = 2:3:3 molar ratio), pH 7.0, 25% w/v PEG 1.500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1808 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 1.91→42.77 Å / Num. obs: 19968 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.066 / Rrim(I) all: 0.17 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.91-1.975.85.0290.317790.2422.2715.53298.6
1.97-2.046.74.5850.418080.071.8974.9799.9
2.04-2.126.82.7810.717860.2621.1493.01399.8
2.12-2.226.61.766118180.3880.7411.918100
2.22-2.346.61.1451.717790.7621.24398.3
2.34-2.486.80.6912.918170.8040.2850.74899.8
2.48-2.686.60.4114.518290.9220.1720.44699.8
2.68-2.946.70.2427.418050.9770.1010.26399.8
2.94-3.376.70.12713.218300.9930.0530.13899.8
3.37-4.256.80.05826.218330.9980.0240.06299.9
4.25-42.776.40.04431.918840.9990.0180.04799.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: 000)refinement
XSCALEdata scaling
PDB_EXTRACTV4.2data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→42.76 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 1573 10.01 %
Rwork0.217 --
obs0.2215 15716 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 79 98 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152138
X-RAY DIFFRACTIONf_angle_d1.6962858
X-RAY DIFFRACTIONf_dihedral_angle_d19.33826
X-RAY DIFFRACTIONf_chiral_restr0.078300
X-RAY DIFFRACTIONf_plane_restr0.013361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.140.36911440.33791287X-RAY DIFFRACTION100
2.14-2.210.35551390.32771261X-RAY DIFFRACTION100
2.21-2.30.49911400.39151248X-RAY DIFFRACTION97
2.3-2.410.28721430.25251299X-RAY DIFFRACTION100
2.41-2.530.28481410.2381261X-RAY DIFFRACTION100
2.53-2.690.3031440.23491296X-RAY DIFFRACTION100
2.69-2.90.27141420.22441277X-RAY DIFFRACTION100
2.9-3.190.25021420.20511277X-RAY DIFFRACTION100
3.19-3.650.24261430.18721293X-RAY DIFFRACTION100
3.65-4.60.19121450.15771304X-RAY DIFFRACTION100
4.6-42.760.26941500.22871340X-RAY DIFFRACTION100

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