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- PDB-1w7v: ZnMg substituted aminopeptidase P from E. coli -

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Basic information

Entry
Database: PDB / ID: 1w7v
TitleZnMg substituted aminopeptidase P from E. coli
Components
  • PEPTIDE VAL-PRO-LEU
  • XAA-PRO AMINOPEPTIDASE
KeywordsHYDROLASE / PROLINE-SPECIFIC PEPTIDASE / METALLOENZYME / PITA-BREAD FOLD / DINUCLEAR HYDROLASE
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGraham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2005
Title: Structural and Functional Implications of Metal Ion Selection in Aminopeptidase P, a Metalloprotease with a Dinuclear Metal Center.
Authors: Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.
History
DepositionSep 13, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 9, 2019Group: Data collection / Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.4Jul 29, 2020Group: Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.5Dec 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XAA-PRO AMINOPEPTIDASE
B: XAA-PRO AMINOPEPTIDASE
C: XAA-PRO AMINOPEPTIDASE
D: XAA-PRO AMINOPEPTIDASE
E: PEPTIDE VAL-PRO-LEU
F: PEPTIDE VAL-PRO-LEU
G: PEPTIDE VAL-PRO-LEU
H: PEPTIDE VAL-PRO-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,02722
Polymers200,4788
Non-polymers54914
Water19,7081094
1
A: XAA-PRO AMINOPEPTIDASE
B: XAA-PRO AMINOPEPTIDASE
E: PEPTIDE VAL-PRO-LEU
F: PEPTIDE VAL-PRO-LEU
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
B: XAA-PRO AMINOPEPTIDASE
E: PEPTIDE VAL-PRO-LEU
F: PEPTIDE VAL-PRO-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,02722
Polymers200,4788
Non-polymers54914
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
2
C: XAA-PRO AMINOPEPTIDASE
D: XAA-PRO AMINOPEPTIDASE
G: PEPTIDE VAL-PRO-LEU
H: PEPTIDE VAL-PRO-LEU
hetero molecules

C: XAA-PRO AMINOPEPTIDASE
D: XAA-PRO AMINOPEPTIDASE
G: PEPTIDE VAL-PRO-LEU
H: PEPTIDE VAL-PRO-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,02722
Polymers200,4788
Non-polymers54914
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)111.731, 236.527, 137.997
Angle α, β, γ (deg.)90.00, 106.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2026-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A6 - 145
2112B6 - 145
3112C6 - 145
4112D6 - 145
1212A147 - 184
2212B147 - 184
3212C147 - 184
4212D147 - 184
1312A186 - 251
2312B186 - 251
3312C186 - 251
4312D186 - 251
1412A254 - 280
2412B254 - 280
3412C254 - 280
4412D254 - 280
1512A282 - 286
2512B282 - 286
3512C282 - 286
4512D282 - 286
1612A288 - 301
2612B288 - 301
3612C288 - 301
4612D288 - 301
1712A306 - 315
2712B306 - 315
3712C306 - 315
4712D306 - 315
1812A317 - 326
2812B317 - 326
3812C317 - 326
4812D317 - 326
1912A328 - 392
2912B328 - 392
3912C328 - 392
4912D328 - 392
11012A400 - 412
21012B400 - 412
31012C400 - 412
41012D400 - 412
11112A418 - 426
21112B418 - 426
31112C418 - 426
41112D418 - 426
11212A430 - 440
21212B430 - 440
31212C430 - 440
41212D430 - 440
DetailsAMINOPEPTIDASE P IS A HOMOTETRAMER IN SOLUTION. HOWEVER,SINCE IN THIS ENTRY, EACH CHAIN OF THIS PROTEIN IS INCOMPLEX WITH A TRIPEPTIDE , THIS ENTRY IS CLASSIFIEDAS A HETEROOCTAMER.

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
XAA-PRO AMINOPEPTIDASE / / X-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P II / APP-II / AMINOACYLPROLINE AMINOPEPTIDASE / AMINOPEPTIDASE P


Mass: 49792.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: AN1459 / Plasmid: PPL670 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase
#2: Protein/peptide
PEPTIDE VAL-PRO-LEU


Mass: 327.419 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: THE PEPTIDE VAL-PRO-LEU (10 MM) WAS SOAKED INTO THE CRYSTALS. THE PEPTIDE WAS CLEAVED BY AMINOPEPTIDASE P, BUT ONE OF THE PRODUCTS (PRO-LEU) REMAINED VISIBLE IN THE ACTIVE SITE
Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 1108 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1094 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYSES THE RELEASE OF ANY N-TERMINAL AMINO ACID, INCLUDING PROLINE, THAT IS LINKED WITH PROLINE, ...CATALYSES THE RELEASE OF ANY N-TERMINAL AMINO ACID, INCLUDING PROLINE, THAT IS LINKED WITH PROLINE, EVEN FROM A DIPEPTIDE OR TRIPEPTIDE.

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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: 4.4 Å3/Da / Density % sol: 71.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.3
Details: ROOM TEMPERATURE HANGING DROP WITH 16% PEG4K, 0.1 M TRIS (PH8.3), 0.2 M MGCL2. TRANSFERRED TO A DROP ABOVE CONDITIONS PLUS WITH 10 MM VAL-PRO-LEU PEPTIDE AND ALLOWED TO EQUILIBRATE OVERNIGHT., pH 8.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.28171
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 1, 2004 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28171 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 225729 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 32.21 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 6 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WL9 WITH ALL HET ATOMS, WATERS AND MULTIPLE CONFORMERS REMOVED

1wl9


Resolution: 2→37.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.503 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSUFFICIENT ELECTRON DENSITY WAS AVAILABLE TO ALLOW COMPLETE MODELLING OF THE RESIDUES A440, B439, B440, C439, C440, D439, D440. RESIDUES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSUFFICIENT ELECTRON DENSITY WAS AVAILABLE TO ALLOW COMPLETE MODELLING OF THE RESIDUES A440, B439, B440, C439, C440, D439, D440. RESIDUES 185 AND 417 IN CHAINS B AND C SHOW CONCERTED MOVEMENT. ONLY ONE OF THE TWO ALTERNATE CONFORMERS OF RESIDUE 417 IN CHAINS B AND C ARE VISIBLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 11297 5 %RANDOM
Rwork0.156 ---
obs0.157 214328 97.9 %-
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: 36.28 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å21.44 Å2
2---0.15 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14028 0 14 1094 15136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02214372
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213108
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.95819455
X-RAY DIFFRACTIONr_angle_other_deg0.762330336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50151757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1323.442738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.084152446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.98115140
X-RAY DIFFRACTIONr_chiral_restr0.0650.22116
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023025
X-RAY DIFFRACTIONr_nbd_refined0.20.22645
X-RAY DIFFRACTIONr_nbd_other0.1770.212601
X-RAY DIFFRACTIONr_nbtor_refined0.1720.26881
X-RAY DIFFRACTIONr_nbtor_other0.080.27796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2847
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.18929497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.689314113
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.87946075
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.97865342
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2393tight positional0.040.05
2B2393tight positional0.030.05
3C2393tight positional0.030.05
4D2393tight positional0.030.05
1A3805medium positional0.120.5
2B3805medium positional0.120.5
3C3805medium positional0.130.5
4D3805medium positional0.120.5
1A2393tight thermal0.090.5
2B2393tight thermal0.10.5
3C2393tight thermal0.080.5
4D2393tight thermal0.10.5
1A3805medium thermal0.52
2B3805medium thermal0.522
3C3805medium thermal0.432
4D3805medium thermal0.512
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.252 811
Rwork0.23 15626
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)
10.9052-0.2848-0.61920.85330.46291.673-0.0702-0.1073-0.03050.02930.0518-0.22970.1770.36030.0184-0.04360.02920.00290.01620.00940.00866.207-16.00616.033
20.89990.2268-0.61211.02580.28021.2632-0.11640.1453-0.0186-0.0884-0.02010.22340.1561-0.26010.1365-0.0908-0.064-0.02130.0074-0.0130.0038-29.051-13.60828.415
30.68450.1835-0.23630.494-0.27531.6477-0.01120.12850.0096-0.12820.02840.13240.0484-0.2635-0.0172-0.0809-0.0105-0.0563-0.02810.0009-0.0759-15.28915.8327.903
40.3798-0.01060.06140.7074-0.33150.8275-0.0023-0.0454-0.0210.0491-0.0424-0.0747-0.12020.07510.0447-0.1191-0.0161-0.0437-0.06660.0078-0.09513.10213.81140.363
50.66160.0781-0.07331.8763-0.21311.4383-0.0213-0.09330.04580.2668-0.0531-0.17940.29430.3290.07450.1310.0528-0.01-0.0149-0.0067-0.0241-3.30355.68155.039
60.55290.0715-0.47161.3916-0.24672.6384-0.18380.1079-0.09240.0244-0.06350.45091.0774-0.64020.24730.6444-0.27010.15590.0501-0.12980.1532-31.04231.76947.53
70.6945-0.0609-0.11371.76540.61171.0771-0.07120.0876-0.0925-0.1091-0.04710.35370.1157-0.18240.1183-0.0921-0.045-0.0433-0.0351-0.04520.0273-24.99781.20447.371
80.68760.22280.15660.78710.39190.6546-0.08490.03580.0077-0.08380.1199-0.0564-0.03510.0956-0.035-0.1472-0.026-0.0303-0.0528-0.0198-0.05821.242105.19858.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 172
2X-RAY DIFFRACTION2A173 - 440
3X-RAY DIFFRACTION3B1 - 172
4X-RAY DIFFRACTION4B173 - 439
5X-RAY DIFFRACTION5C1 - 172
6X-RAY DIFFRACTION6C173 - 439
7X-RAY DIFFRACTION7D1 - 172
8X-RAY DIFFRACTION8D173 - 439

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