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

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Basic information

Entry
Database: PDB / ID: 1wbq
TitleZnMg substituted aminopeptidase P from E. coli
ComponentsXAA-PRO AMINOPEPTIDASE
KeywordsHYDROLASE / PROLINE-SPECIFIC PEPTIDASE / METALLOENZYME / PITA-BREAD FOLD / DINUCLEAR HYDROLASE / METAL BINDING PROTEIN
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 ...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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionNov 5, 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 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,71818
Polymers199,1684
Non-polymers54914
Water14,988832
1
A: XAA-PRO AMINOPEPTIDASE
B: XAA-PRO AMINOPEPTIDASE
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
B: XAA-PRO AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,71818
Polymers199,1684
Non-polymers54914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
2
C: XAA-PRO AMINOPEPTIDASE
D: XAA-PRO AMINOPEPTIDASE
hetero molecules

C: XAA-PRO AMINOPEPTIDASE
D: XAA-PRO AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,71818
Polymers199,1684
Non-polymers54914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)111.974, 236.703, 137.637
Angle α, β, γ (deg.)90.00, 106.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2021-

HOH

21D-2125-

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 - 51
2112B6 - 51
3112C6 - 51
4112D6 - 51
1214A52 - 54
2214B52 - 54
3214C52 - 54
4214D52 - 54
1312A55 - 145
2312B55 - 145
3312C55 - 145
4312D55 - 145
1412A147 - 184
2412B147 - 184
3412C147 - 184
4412D147 - 184
1512A186 - 251
2512B186 - 251
3512C186 - 251
4512D186 - 251
1612A254 - 280
2612B254 - 280
3612C254 - 280
4612D254 - 280
1712A282 - 286
2712B282 - 286
3712C282 - 286
4712D282 - 286
1812A288 - 301
2812B288 - 301
3812C288 - 301
4812D288 - 301
1912A306 - 315
2912B306 - 315
3912C306 - 315
4912D306 - 315
11012A317 - 326
21012B317 - 326
31012C317 - 326
41012D317 - 326
11112A328 - 344
21112B328 - 344
31112C328 - 344
41112D328 - 344
11212A346 - 392
21212B346 - 392
31212C346 - 392
41212D346 - 392
11312A400 - 412
21312B400 - 412
31312C400 - 412
41312D400 - 412
11412A418 - 426
21412B418 - 426
31412C418 - 426
41412D418 - 426
11512A430 - 440
21512B430 - 440
31512C430 - 440
41512D430 - 440
DetailsAMINOPEPTIDASE P IS A HOMOTETRAMER IN SOLUTION.

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Components

#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) / Plasmid: PPL670 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: RELEASE OF ANY N-TERMINAL AMINO ACID, INCLUDING PROLINE, THAT IS LINKED WITH ...CATALYTIC ACTIVITY: 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: 68.2 %
Description: STARTING MODEL WAS A TETRAMER OF 1WL9 GENERATED BY CRYSTALLOGRAPHIC OPERATORS STRIPPED OF ANY MULTIPLE CONFORMERS OR HETERO COMPOUNDS
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. CRYOPROTECTED WITH 10-15% MPD., pH 8.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 21, 2004 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.97 Å / Num. obs: 150167 / % possible obs: 98.9 % / Observed criterion σ(I): -3.7 / Redundancy: 2.8 % / Biso Wilson estimate: 35.89 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.62
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.4 / % possible all: 97.6

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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

1wl9


Resolution: 2.3→29.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.877 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 7512 5 %RANDOM
Rwork0.167 ---
obs0.168 142654 98.9 %-
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: 35.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20.94 Å2
2---0.1 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13964 0 14 832 14810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02214256
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212959
X-RAY DIFFRACTIONr_angle_refined_deg1.071.95519318
X-RAY DIFFRACTIONr_angle_other_deg0.763329995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70651753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32723.571728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.294152421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.93315132
X-RAY DIFFRACTIONr_chiral_restr0.0620.22105
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022989
X-RAY DIFFRACTIONr_nbd_refined0.1970.22747
X-RAY DIFFRACTIONr_nbd_other0.1720.212873
X-RAY DIFFRACTIONr_nbtor_refined0.170.26848
X-RAY DIFFRACTIONr_nbtor_other0.0790.28287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2749
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5729428
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.238314038
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.15646012
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.24665280
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
1A2370tight positional0.030.05
2B2370tight positional0.030.05
3C2370tight positional0.020.05
4D2370tight positional0.030.05
1A3778medium positional0.130.5
2B3778medium positional0.120.5
3C3778medium positional0.130.5
4D3778medium positional0.130.5
1A2370tight thermal0.070.5
2B2370tight thermal0.080.5
3C2370tight thermal0.060.5
4D2370tight thermal0.080.5
1A3778medium thermal0.532
2B3778medium thermal0.522
3C3778medium thermal0.462
4D3778medium thermal0.512
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 522
Rwork0.232 10283
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)
10.8917-0.1838-0.68310.66730.30141.8511-0.0574-0.1495-0.02280.05390.0421-0.20690.12060.42040.0152-0.04590.01920.00040.0164-0.0023-0.0086.3067-15.976515.9723
20.86560.1873-0.57580.98070.34711.2633-0.10170.1634-0.0001-0.117-0.02220.21180.1377-0.25350.1239-0.0979-0.067-0.0236-0.0023-0.0079-0.0203-28.8913-13.547628.4646
30.74810.1681-0.22230.5658-0.22211.8419-0.01260.1-0.0153-0.09060.01630.14360.0634-0.292-0.0037-0.0985-0.0182-0.0455-0.04840.0026-0.0968-15.238715.87797.9695
40.3646-0.04080.09260.7536-0.40090.73070.0062-0.0311-0.01670.0459-0.0465-0.0647-0.10930.06430.0403-0.137-0.0165-0.0298-0.07470.0019-0.12033.335613.791540.304
50.54550.0326-0.04661.8496-0.00121.1073-0.0257-0.07690.03010.3288-0.0059-0.21460.30640.29260.03160.13810.039-0.0152-0.0151-0.0123-0.0471-3.00255.75454.9615
60.71220.0541-0.36541.3546-0.2532.4226-0.15520.0479-0.10560.0509-0.04830.45040.9223-0.62270.20350.556-0.24310.16620.0532-0.12250.134-30.743231.828647.4739
70.6119-0.134-0.11191.98140.6551.2447-0.0740.1064-0.0584-0.0777-0.05940.4090.0928-0.19930.1335-0.1116-0.0433-0.0282-0.0449-0.04820.0179-24.781.279447.3098
80.73410.19980.12550.72510.40260.7088-0.08680.04290.009-0.08410.1155-0.0513-0.02490.0945-0.0288-0.1602-0.0216-0.0216-0.0812-0.0145-0.07961.5427105.279958.8102
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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