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- PDB-8vpm: Glutaminyl cyclase ApgG, rod shape -

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Basic information

Entry
Database: PDB / ID: 8vpm
TitleGlutaminyl cyclase ApgG, rod shape
ComponentsPeptide hydrolase
KeywordsTRANSFERASE / Glutaminyl cyclase
Function / homology
Function and homology information


glutaminyl-peptide cyclotransferase activity / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / proteolysis / zinc ion binding
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsNie, Q. / Chang, C. / Gao, Y. / Gao, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R23490 United States
CitationJournal: To Be Published
Title: Glutaminyl cyclase ApgG, rod shape
Authors: Nie, Q. / Chang, C. / Gao, Y. / Gao, X.
History
DepositionJan 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 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: Peptide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1992
Polymers39,1341
Non-polymers651
Water362
1
A: Peptide hydrolase
hetero molecules

A: Peptide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3984
Polymers78,2672
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area2370 Å2
ΔGint-62 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.947, 123.947, 46.076
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Peptide hydrolase


Mass: 39133.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: F9C07_6934 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7U2MGR8, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 55.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Bis-Tris (pH 6.5), PEG 10000, and 0.2 M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.15→42.34 Å / Num. obs: 42880 / % possible obs: 99.6 % / Redundancy: 11.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.094 / Net I/σ(I): 12.39
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.15-2.280.7369400.7910.8021
2.28-2.440.4364850.9160.4721
2.44-2.630.26660180.9720.2921
2.63-2.880.16556110.9850.1811
2.88-3.220.10550400.9930.1161
3.22-3.720.07244430.9950.0791
3.72-4.540.06137800.9960.0671
4.54-6.390.05729270.9960.0631
6.39-42.340.05616360.9960.0611

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→42.34 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 1133 5.09 %
Rwork0.2124 --
obs0.2141 22280 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 1 2 2626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012691
X-RAY DIFFRACTIONf_angle_d1.1613672
X-RAY DIFFRACTIONf_dihedral_angle_d16.142957
X-RAY DIFFRACTIONf_chiral_restr0.067413
X-RAY DIFFRACTIONf_plane_restr0.009474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.250.32331470.27572611X-RAY DIFFRACTION100
2.25-2.370.32861210.25212646X-RAY DIFFRACTION100
2.37-2.520.31361410.27142603X-RAY DIFFRACTION100
2.52-2.710.34211640.26912635X-RAY DIFFRACTION100
2.71-2.980.32791380.26552608X-RAY DIFFRACTION100
2.98-3.410.25581210.23422663X-RAY DIFFRACTION100
3.41-4.30.20171330.19482675X-RAY DIFFRACTION100
4.3-42.340.20091680.16282706X-RAY DIFFRACTION100

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