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- PDB-1p3c: Glutamyl endopeptidase from Bacillus intermedius -

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Basic information

Entry
Database: PDB / ID: 1p3c
TitleGlutamyl endopeptidase from Bacillus intermedius
Componentsglutamyl-endopeptidase
KeywordsHYDROLASE / serine protease
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: 1.5 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 / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 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: glutamyl-endopeptidase


Theoretical massNumber of molelcules
Total (without water)22,7831
Polymers22,7831
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.494, 85.437, 82.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.06 Å3/Da / Density % sol: 39.72 %
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, 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: Jan 15, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→19.5 Å / Num. all: 33771 / Num. obs: 33011 / % possible obs: 97.3 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -3
Reflection shellResolution: 1.5→1.54 Å / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AGJ

1agj


Resolution: 1.5→19.32 Å / Cor.coef. Fo:Fc: 0.98 / SU B: 0.822 / SU ML: 0.03 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -2 / ESU R: 0.055 / 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
Rfree0.184 1132 -random
Rwork0.153 ---
all0.158 33771 --
obs0.156 33010 97.56 %-
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: 14.392 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--0.19 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 0 155 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211698
X-RAY DIFFRACTIONr_bond_other_d0.0020.021466
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9282323
X-RAY DIFFRACTIONr_angle_other_deg0.82633426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3885232
X-RAY DIFFRACTIONr_chiral_restr0.0970.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021976
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02351
X-RAY DIFFRACTIONr_nbd_refined0.1860.2265
X-RAY DIFFRACTIONr_nbd_other0.2470.21666
X-RAY DIFFRACTIONr_nbtor_other0.0830.21024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3810.213
X-RAY DIFFRACTIONr_mcbond_it0.9141.51093
X-RAY DIFFRACTIONr_mcangle_it1.71821773
X-RAY DIFFRACTIONr_scbond_it2.5743605
X-RAY DIFFRACTIONr_scangle_it4.2164.5544
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.193 2324
Rfree-0
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)
10.4182-0.1252-0.03220.2314-0.08870.2740.00350.1012-0.0523-0.0082-0.0252-0.00720.0162-0.01930.02170.0133-0.00180.00810.0162-0.00390.005511.480427.41949.9506
20.5529-0.0424-0.03770.0589-0.09410.2991-0.0029-0.04650.01960.02170.0005-0.0115-0.03420.01050.00240.01630.00040.00350.00590.00010.012215.74133.292823.9144
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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