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- PDB-1p3e: Structure of Glu endopeptidase in complex with MPD -

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Basic information

Entry
Database: PDB / ID: 1p3e
TitleStructure of Glu endopeptidase in complex with MPD
Componentsglutamyl-endopeptidase
KeywordsHYDROLASE / serine protease / Glu specific
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S1B / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus intermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMeijers, R. / Blagova, E.V. / Levdikov, V.M. / Rudenskaya, G.N. / Chestukhina, G.G. / Akimkina, T.V. / Kostrov, S.V. / Lamzin, V.S. / Kuranova, I.P.
CitationJournal: Biochemistry / Year: 2004
Title: The crystal structure of glutamyl endopeptidase from Bacillus intermedius reveals a structural link between zymogen activation and charge compensation.
Authors: Meijers, R. / Blagova, E.V. / Levdikov, V.M. / Rudenskaya, G.N. / Chestukhina, G.G. / Akimkina, T.V. / Kostrov, S.V. / Lamzin, V.S. / Kuranova, I.P.
History
DepositionApr 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutamyl-endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9012
Polymers22,7831
Non-polymers1181
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: glutamyl-endopeptidase
hetero molecules

A: glutamyl-endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8034
Polymers45,5662
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2980 Å2
ΔGint-36 kcal/mol
Surface area15150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.936, 55.757, 60.195
Angle α, β, γ (deg.)90.00, 118.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

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Components

#1: Protein glutamyl-endopeptidase


Mass: 22783.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus intermedius (bacteria) / Strain: 3-19 / References: UniProt: Q9EXR9
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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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: 1.85 Å3/Da / Density % sol: 33.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.01 M Tris-HCl buffer, pH 7.0, 2 mM CaCl2, 1.2 M potassium phosphate, 3% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1999
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.72→20 Å / Num. all: 18778 / Num. obs: 18778 / % possible obs: 93 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -3
Reflection shellResolution: 1.72→1.76 Å / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P3C

1p3c


Resolution: 1.72→19.69 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.465 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO REFLECTIONS WERE EXCLUDED ON THE BASIS OF A SIGMA CUTOFF
RfactorNum. reflection% reflectionSelection details
Rfree0.20809 965 5.2 %RANDOM
Rwork0.16579 ---
all0.16791 17769 --
obs0.16791 17769 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.378 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å21.84 Å2
2---0.23 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.72→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 8 124 1732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211674
X-RAY DIFFRACTIONr_bond_other_d0.0020.021452
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9292283
X-RAY DIFFRACTIONr_angle_other_deg1.19133382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825222
X-RAY DIFFRACTIONr_chiral_restr0.1210.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021933
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02341
X-RAY DIFFRACTIONr_nbd_refined0.1830.2298
X-RAY DIFFRACTIONr_nbd_other0.2450.21683
X-RAY DIFFRACTIONr_nbtor_other0.0850.21013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3610.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.28
X-RAY DIFFRACTIONr_mcbond_it0.8771.51080
X-RAY DIFFRACTIONr_mcangle_it1.55721745
X-RAY DIFFRACTIONr_scbond_it2.3013594
X-RAY DIFFRACTIONr_scangle_it3.7344.5538
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 51
Rwork0.223 1255
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)
1-0.106-0.0839-0.24261.12440.1192-0.080.1260.0596-0.1331-0.1290.00840.06080.1016-0.0792-0.13440.12860.04330.04070.25040.04120.088711.4827.4199.951
2-0.2499-0.5289-0.15550.90340.2604-0.41260.03060.0656-0.227-0.01570.009-0.19460.28540.1667-0.03950.0576-0.1034-0.01420.19150.04280.054115.74133.29323.914
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 211 - 21
2X-RAY DIFFRACTION1AA122 - 200122 - 200
3X-RAY DIFFRACTION2AA22 - 12122 - 121
4X-RAY DIFFRACTION2AA201 - 215201 - 215

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