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- PDB-1m22: X-ray structure of native peptide amidase from Stenotrophomonas m... -

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Basic information

Entry
Database: PDB / ID: 1m22
TitleX-ray structure of native peptide amidase from Stenotrophomonas maltophilia at 1.4 A
Componentspeptide amidase
KeywordsHYDROLASE / eleven-stranded beta sheet / covered double layers of alpha helices on top and bottom
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
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.4 Å
AuthorsLabahn, J. / Neumann, S. / Buldt, G. / Kula, M.-R. / Granzin, J.
Citation
Journal: J.MOL.BIOL. / Year: 2002
Title: An alternative mechanism for amidase signature enzymes
Authors: Labahn, J. / Neumann, S. / Buldt, G. / Kula, M.-R. / Granzin, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary X-ray data of the recombinant peptide amidase from Stenotrophomonas maltophilia
Authors: Neumann, S. / Granzin, J. / Kula, M.-R. / Labahn, J.
#2: Journal: Appl.Microbiol.Biotechnol. / Year: 1995
Title: Purification and characterisation of a newly screened microbial peptide amidase
Authors: Stelkes-Ritter, U. / Wyzgol, K. / Kula, M.-R.
History
DepositionJun 21, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / refine / struct_biol
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _refine.ls_R_factor_all
Revision 1.4Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: peptide amidase
B: peptide amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5674
Polymers107,0912
Non-polymers4772
Water20,6991149
1
A: peptide amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7842
Polymers53,5451
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: peptide amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7842
Polymers53,5451
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.179, 62.596, 101.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological unit is the monomer

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Components

#1: Protein peptide amidase / PAM


Mass: 53545.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Plasmid: pEK06 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RJN5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1149 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG6000, Hepes Glycerine Sodium Azide, pH 7.5, vapour diffusion, sitting drop, temperature 289K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: Neumann, S., (2002) Acta Crystallogr., Sect.D, 58, 333.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113 %PEG60001reservoir
20.1 MHEPES1reservoirpH7.5
320 %glycerine1reservoir
40.02 %sodium azide1reservoir
524 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2001
RadiationMonochromator: diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→79 Å / Num. all: 182206 / Num. obs: 182206 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.8
Reflection shellResolution: 1.4→1.49 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.1 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 79 Å / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.169

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.4→79 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 8947 4.9 %RANDOM
Rwork0.188 ---
obs0.188 182174 99 %-
all-182206 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5075 Å2 / ksol: 0.380289 e/Å3
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.4→79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7298 0 30 1149 8477
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.22.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 1481 5 %
Rwork0.25 28014 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2EPE_XPLOR_PARAMEPE_XPLOR_TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 100 Å / Rfactor all: 0.18 / Rfactor obs: 0.189 / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.371
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.26 / Rfactor Rwork: 0.25

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