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- PDB-1m21: Crystal structure analysis of the peptide amidase PAM in complex ... -

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Basic information

Entry
Database: PDB / ID: 1m21
TitleCrystal structure analysis of the peptide amidase PAM in complex with the competitive inhibitor chymostatin
Components
  • CHYMOSTATIN
  • Peptide Amidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein-Inhibitor Complex / core: eleven-stranded beta-sheet / covered: double layers of alpha helices on top and bottom / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
Chymostatin A / Amidase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
Streptomyces hygroscopicus (bacteria)
MC521-C8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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.
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: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 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
B: Peptide Amidase
C: CHYMOSTATIN
D: CHYMOSTATIN


Theoretical massNumber of molelcules
Total (without water)108,3064
Polymers108,3064
Non-polymers00
Water7,764431
1
A: Peptide Amidase
C: CHYMOSTATIN


Theoretical massNumber of molelcules
Total (without water)54,1532
Polymers54,1532
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-10 kcal/mol
Surface area17340 Å2
MethodPISA
2
B: Peptide Amidase
D: CHYMOSTATIN


Theoretical massNumber of molelcules
Total (without water)54,1532
Polymers54,1532
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-10 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.598, 62.559, 102.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Detailstwo biological entities are in the asym. unit

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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: Protein/peptide CHYMOSTATIN


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 607.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces hygroscopicus, MC521-C8 / References: Chymostatin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG6000, HEPES, Glycerine, Sodium Azide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal grow
*PLUS
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: 1.8→60.29 Å / Num. all: 87122 / Num. obs: 87122 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.085 / Net I/σ(I): 6.1
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3 / Rsym value: 0.207 / % possible all: 79.9
Reflection
*PLUS
Highest resolution: 1.78 Å / Num. obs: 89189 / % possible obs: 98.1 % / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 79.9 % / Rmerge(I) obs: 0.273

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M22

1m22


Resolution: 1.8→60.29 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4379 5 %RANDOM
Rwork0.203 ---
all0.203 87122 --
obs0.203 87122 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5977 Å2 / ksol: 0.386826 e/Å3
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.8→60.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7390 0 0 431 7821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it0.91.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 682 4.7 %
Rwork0.226 13762 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CTC.PARAMCTC.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.389
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.247 / Rfactor Rwork: 0.226

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