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- PDB-4dyo: Crystal Structure of Human Aspartyl Aminopeptidase (DNPEP) in com... -

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Basic information

Entry
Database: PDB / ID: 4dyo
TitleCrystal Structure of Human Aspartyl Aminopeptidase (DNPEP) in complex with Aspartic acid Hydroxamate
ComponentsAspartyl aminopeptidase
KeywordsHYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


aspartyl aminopeptidase / peptide metabolic process / aminopeptidase activity / metallopeptidase activity / blood microparticle / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Aminopeptidase i, Domain 2 / Aminopeptidase i, Domain 2 / Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18) / Zn peptidases / Aminopeptidase / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-hydroxy-L-asparagine / Aspartyl aminopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChaikuad, A. / Pilka, E. / Vollmar, M. / Krojer, T. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Chaikuad, A. / Pilka, E. / Vollmar, M. / Krojer, T. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Bmc Struct.Biol. / Year: 2012
Title: Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family.
Authors: Chaikuad, A. / Pilka, E.S. / Riso, A.D. / Delft, F.V. / Kavanagh, K.L. / Venien-Bryan, C. / Oppermann, U. / Yue, W.W.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMar 14, 2012ID: 3L6S
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,42111
Polymers53,5651
Non-polymers85610
Water5,783321
1
A: Aspartyl aminopeptidase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)653,054132
Polymers642,78412
Non-polymers10,270120
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation51_555-x+1/2,y,-z+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation74_555-x+1/2,-y+1/2,z1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
2
A: Aspartyl aminopeptidase
hetero molecules

A: Aspartyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,84222
Polymers107,1312
Non-polymers1,71220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
Buried area7860 Å2
ΔGint-75 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.595, 244.595, 244.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-503-

MG

21A-777-

HOH

31A-812-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aspartyl aminopeptidase / / DNPEP


Mass: 53565.355 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPEP, DAP, DNPEP / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q9ULA0, aspartyl aminopeptidase

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Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SD4 / N-hydroxy-L-asparagine


Type: L-peptide linking / Mass: 148.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES -9 THROUGH 0 ARE A NATURAL EXPRESSION TAG (AS PER UNP Q53SB6).

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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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% PEG3350, 0.25 M magnesium chloride, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2009 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→56.11 Å / Num. all: 32192 / Num. obs: 32185 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.179 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4486 / % possible all: 97.5

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IJZ

2ijz


Resolution: 2.2→54.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.835 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.177 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1230 3.8 %RANDOM
Rwork0.1547 ---
obs0.156 30955 99.5 %-
all-32185 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.863 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: LAST / Resolution: 2.2→54.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 49 321 3901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223716
X-RAY DIFFRACTIONr_bond_other_d0.0010.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.975028
X-RAY DIFFRACTIONr_angle_other_deg0.93236217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4523.758165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79415626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8241528
X-RAY DIFFRACTIONr_chiral_restr0.0950.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_mcbond_it2.78132318
X-RAY DIFFRACTIONr_mcbond_other0.8673931
X-RAY DIFFRACTIONr_mcangle_it4.21753746
X-RAY DIFFRACTIONr_scbond_it7.21181398
X-RAY DIFFRACTIONr_scangle_it9.385111274
X-RAY DIFFRACTIONr_sphericity_free40.49831
X-RAY DIFFRACTIONr_sphericity_bonded3.03132
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 75 -
Rwork0.241 2151 -
obs--95.74 %
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)
10.3716-0.3307-0.01881.04570.20870.29620.01040.03010.0216-0.0595-0.0114-0.0807-0.02480.04190.0010.0366-0.0136-0.0010.06080.0050.0454104.204851.59145.6356
22.44460.71720.24262.03732.0462.1782-0.04590.20160.0182-0.33090.124-0.1135-0.3210.109-0.07810.16810.00230.08130.08170.05280.1255106.803273.911639.4863
30.37550.04560.03640.43740.11130.5377-0.00130.0193-0.0389-0.00040.0014-0.03690.06670.032-0.00010.03860.0035-0.00060.04410.00080.0531100.411735.92551.5762
430.433410.69123.06684.0824-0.27775.9424-0.1727-0.1108-0.7681-0.33620.007-0.32461.1004-0.25650.16570.4066-0.00270.1360.2578-0.20350.7048101.800913.4550.688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 190
2X-RAY DIFFRACTION2A191 - 230
3X-RAY DIFFRACTION3A231 - 467
4X-RAY DIFFRACTION4A468 - 473

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