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- PDB-6gmg: Structure of a glutamine donor mimicking inhibitory peptide shape... -

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Basic information

Entry
Database: PDB / ID: 6gmg
TitleStructure of a glutamine donor mimicking inhibitory peptide shaped by the catalytic cleft of microbial transglutaminase
Components
  • PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
  • Papain inhibitor
KeywordsTRANSFERASE / transglutaminase / Streptomyces mobaraensis / peptidic inhibitors / enzyme peptide interaction
Function / homology
Function and homology information


negative regulation of peptidase activity / protein-glutamine gamma-glutamyltransferase activity / cysteine-type endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
: / Microbial transglutaminase. Chain: a / Protein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase superfamily / Microbial transglutaminase / : / RlpA-like protein, double-psi beta-barrel domain / Lytic transglycolase / RlpA-like domain superfamily ...: / Microbial transglutaminase. Chain: a / Protein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase superfamily / Microbial transglutaminase / : / RlpA-like protein, double-psi beta-barrel domain / Lytic transglycolase / RlpA-like domain superfamily / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / DI(HYDROXYETHYL)ETHER / Protein-glutamine gamma-glutamyltransferase / Papain inhibitor
Similarity search - Component
Biological speciesStreptomyces mobaraensis NBRC 13819 = DSM 40847 (bacteria)
Streptomyces mobaraensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSchmelz, S. / Juettner, N.E. / Fuchsbauer, H.L. / Scrima, A.
CitationJournal: FEBS J. / Year: 2018
Title: Structure of a glutamine donor mimicking inhibitory peptide shaped by the catalytic cleft of microbial transglutaminase.
Authors: Juettner, N.E. / Schmelz, S. / Kraemer, A. / Knapp, S. / Becker, B. / Kolmar, H. / Scrima, A. / Fuchsbauer, H.L.
History
DepositionMay 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
B: PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
C: Papain inhibitor
D: Papain inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,56510
Polymers77,8454
Non-polymers7206
Water4,990277
1
A: PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
C: Papain inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3245
Polymers38,9232
Non-polymers4013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
D: Papain inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2415
Polymers38,9232
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.525, 85.492, 78.793
Angle α, β, γ (deg.)90.000, 111.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE


Mass: 37918.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Streptomyces mobaraensis NBRC 13819 = DSM 40847 (bacteria)
References: UniProt: M3C567
#2: Protein/peptide Papain inhibitor / SPI


Mass: 1004.178 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: chloroacetylated serine peptide derived from SPI aa1-10, Glutamin6 was replace by a chloroacetylated serine
Source: (synth.) Streptomyces mobaraensis (bacteria) / References: UniProt: P86242*PLUS
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 38% v/v PEG400, 70 mM di-Sodium hydrogen phosphate, 100 mM Sodium phosphate citrate, pH 4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→47 Å / Num. obs: 35089 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.71 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.08 / Rrim(I) all: 0.212 / Net I/σ(I): 8.1 / Num. measured all: 241385 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.326.80.9022174731960.8090.3660.9752.298.2
9-477.20.07441885800.9970.0290.07920.599.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å46.99 Å
Translation2.4 Å46.99 Å

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Processing

Software
NameVersionClassification
PHENIXdev_3112refinement
XDSBUILT=20180126data reduction
Aimless0.7.1data scaling
PHASER2.7.18phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iu4

1iu4


Resolution: 2.25→47.001 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 1754 5 %
Rwork0.222 33293 -
obs0.2248 35047 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.05 Å2 / Biso mean: 25.9491 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 2.25→47.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 48 277 5782
Biso mean--31.76 24.75 -
Num. residues----678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.31090.33451320.26952509264198
2.3109-2.37890.34351340.26192536267098
2.3789-2.45570.2991320.2732528266098
2.4557-2.54340.3571340.26832546268098
2.5434-2.64520.34511340.25612550268499
2.6452-2.76560.2851350.24822548268399
2.7656-2.91140.31571350.24932560269599
2.9114-3.09380.29761340.24262551268599
3.0938-3.33260.2771350.24472563269899
3.3326-3.66790.29381350.20892564269999
3.6679-4.19830.24541370.18292597273499
4.1983-5.28830.19951370.1742595273299
5.2883-47.0110.24531400.19882646278699

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