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- PDB-5ac3: Crystal structure of PAM12A -

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Basic information

Entry
Database: PDB / ID: 5ac3
TitleCrystal structure of PAM12A
ComponentsPEPTIDE AMIDASE
KeywordsHYDROLASE / MUTAGENESIS
Function / homology
Function and homology information


amidase / hydrolase activity
Similarity search - Function
Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / Amidase
Similarity search - Component
Biological speciesSTENOTROPHOMONAS MALTOPHILIA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWu, B. / Wijma, H.J. / Song, L. / Rozeboom, H.J. / Poloni, C. / Tian, Y. / Arif, M.I. / Nuijens, T. / Quadflieg, P.J.L.M. / Szymanski, W. ...Wu, B. / Wijma, H.J. / Song, L. / Rozeboom, H.J. / Poloni, C. / Tian, Y. / Arif, M.I. / Nuijens, T. / Quadflieg, P.J.L.M. / Szymanski, W. / Feringa, B.L. / Janssen, D.B.
CitationJournal: Acs Catalysis / Year: 2016
Title: Versatile Peptide C-Terminal Functionalization Via a Computationally Peptide Amidase
Authors: Wu, B. / Wijma, H.J. / Song, L. / Rozeboom, H.J. / Poloni, C. / Tian, Y. / Arif, M.I. / Nuijens, T. / Quadflieg, P.J.L.M. / Szymanski, W. / Feringa, B.L. / Janssen, D.B.
History
DepositionAug 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Jan 10, 2024Group: 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 / struct_site
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_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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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
A: PEPTIDE AMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,30315
Polymers54,9911
Non-polymers1,31214
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.870, 82.870, 112.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1537-

CD

21A-2143-

HOH

31A-2338-

HOH

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Components

#1: Protein PEPTIDE AMIDASE


Mass: 54990.926 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STENOTROPHOMONAS MALTOPHILIA (bacteria)
Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): TOP10 / References: UniProt: Q8RJN5, amidase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: VAPOR DIFFUSION, HANGING DROP, 1.0 M SODIUM ACETATE, 0.1 M HEPES PH 7.0, 0.02M CADMIUM SULFATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 17, 2014 / Details: HELIOSMX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→41.4 Å / Num. obs: 42172 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M22

1m22


Resolution: 1.8→71.77 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.394 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19608 2108 5 %RANDOM
Rwork0.15975 ---
obs0.16159 40001 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→71.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 29 340 4055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193789
X-RAY DIFFRACTIONr_bond_other_d0.0010.023632
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.985161
X-RAY DIFFRACTIONr_angle_other_deg0.78638325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.79122.547161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80815575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7831541
X-RAY DIFFRACTIONr_chiral_restr0.0690.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02847
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_it0.6961.2391969
X-RAY DIFFRACTIONr_mcbond_other0.6731.2321963
X-RAY DIFFRACTIONr_mcangle_it1.1581.8442455
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0511.4351820
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 146 -
Rwork0.253 2935 -
obs--99.94 %
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)
11.0526-0.7488-0.07142.74870.3410.7013-0.03660.1697-0.0350.04030.0445-0.0370.13080.0105-0.00790.0602-0.0174-0.00470.0974-0.02030.032315.8428-43.5882-24.4273
20.61920.09470.19520.56370.07610.5634-0.00840.06930.03090.01290.0218-0.04660.00090.0343-0.01340.0513-0.01280.00930.08070.00180.07119.9508-29.5216-14.8687
30.81940.2498-0.11720.4008-0.03650.49120.0068-0.0060.13110.04660.00170.0374-0.088-0.0279-0.00850.05650.00160.00120.0352-0.00150.075412.1453-19.6143-7.5615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 107
2X-RAY DIFFRACTION2A108 - 305
3X-RAY DIFFRACTION3A306 - 531

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