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- PDB-4hxf: Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethy... -

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Basic information

Entry
Database: PDB / ID: 4hxf
TitleAcylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethyl ketone
ComponentsPutative uncharacterized protein PH0594
KeywordsHYDROLASE/HYDROLASE INHIBITOR / self-compartmentalization / beta-propeller / alpha/beta hyrdolase fold / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
WD40-like beta propeller / WD40-like Beta Propeller Repeat / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Six-bladed beta-propeller, TolB-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM) / HEXANE-1,6-DIOL / Chem-Y3A / Peptidase S9 prolyl oligopeptidase catalytic domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsKiss-Szeman, A. / Menyhard, D.K. / Tichy-Racs, E. / Hornung, B. / Radi, K. / Szeltner, Z. / Domokos, K. / Szamosi, I. / Naray-Szabo, G. / Polgar, L. / Harmat, V.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: A Self-compartmentalizing Hexamer Serine Protease from Pyrococcus Horikoshii: SUBSTRATE SELECTION ACHIEVED THROUGH MULTIMERIZATION.
Authors: Menyhard, D.K. / Kiss-Szeman, A. / Tichy-Racs, E. / Hornung, B. / Radi, K. / Szeltner, Z. / Domokos, K. / Szamosi, I. / Naray-Szabo, G. / Polgar, L. / Harmat, V.
#1: Journal: Biochim.Biophys.Acta / Year: 2009
Title: Characterization of a novel acylaminoacyl peptidase with hexameric structure and endopeptidase activity.
Authors: Szeltner, Z. / Kiss, A.L. / Domokos, K. / Harmat, V. / Naray-Szabo, G. / Polgar, L.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Oct 8, 2014Group: Non-polymer description
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_molecule / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_molecule.prd_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 18, 2023Group: Structure summary / Category: pdbx_molecule / Item: _pdbx_molecule.prd_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Putative uncharacterized protein PH0594
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,12318
Polymers73,3361
Non-polymers1,78717
Water11,800655
1
B: Putative uncharacterized protein PH0594
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)450,737108
Polymers440,0186
Non-polymers10,720102
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area48050 Å2
ΔGint-145 kcal/mol
Surface area120550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.057, 184.057, 145.529
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-1120-

HOH

21B-1429-

HOH

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Putative uncharacterized protein PH0594


Mass: 73336.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0594 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O58323, acylaminoacyl-peptidase

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Non-polymers , 5 types, 672 molecules

#2: Chemical ChemComp-Y3A / N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide / Z-Gly-Gly-Phe-Chloromethyl ketone (bound form)


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 447.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26ClN3O5
Details: The chlorormethyl ketone inhibitor linked to the protein through two covalent bonds with the active site serine and histidine
References: Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.5 M 1,6-hexanediol, 0.20 M MgCl2, 0.1 M Tris/HCl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2010 / Details: confocal mirrors
RadiationMonochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 122438 / Num. obs: 122438 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.03 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.25
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 5.24 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 2.57 / % possible all: 94.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HXE

4hxe


Resolution: 1.601→19.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.824 / SU ML: 0.048 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HEZ B711 AND WATER B1336 LIE ON A TWOFOLD AXIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 6218 5.1 %RANDOM
Rwork0.15457 ---
obs0.15617 116219 99.22 %-
all-116219 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.601→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5019 0 102 655 5776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.025327
X-RAY DIFFRACTIONr_bond_other_d0.0010.023806
X-RAY DIFFRACTIONr_angle_refined_deg2.2481.9637178
X-RAY DIFFRACTIONr_angle_other_deg1.10839201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56223.65263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59715919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0171533
X-RAY DIFFRACTIONr_chiral_restr0.1440.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021195
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 447 -
Rwork0.29 7838 -
obs--94.19 %
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)
10.53090.0677-0.08010.32780.02160.5254-0.02320.0281-0.0906-0.01940.0063-0.06210.07020.05750.01690.04790.00240.00090.0364-0.00180.0249-7.809-44.726-14.592
20.21410.0621-0.03370.2842-0.02140.12880.0030.04270.0218-0.02290.01650.01040.001-0.0249-0.01950.0851-0.0122-0.01870.08660.00730.0101-18.5-20.895-29.552
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B4 - 12
2X-RAY DIFFRACTION1B345 - 618
3X-RAY DIFFRACTION2B13 - 344

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