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- PDB-1o9n: Crystal structure of the K62A mutant of Malonamidase E2 from Brad... -

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Basic information

Entry
Database: PDB / ID: 1o9n
TitleCrystal structure of the K62A mutant of Malonamidase E2 from Bradyrhizobium japonicum
ComponentsMALONAMIDASE E2
KeywordsAMIDASE / MALONAMIDASE / MUTANT
Function / homology
Function and homology information


Amidase / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesBRADYRHIZOBIUM JAPONICUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShin, S. / Oh, B.-H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Characterization of a Novel Ser-Cisser-Lys Catalytic Triad in Comparison with the Classical Ser-His-Asp Triad
Authors: Shin, S. / Yun, Y.S. / Koo, H.M. / Kim, Y.S. / Choi, K.Y. / Oh, B.-H.
History
DepositionDec 18, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 6, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
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: MALONAMIDASE E2
B: MALONAMIDASE E2


Theoretical massNumber of molelcules
Total (without water)87,3552
Polymers87,3552
Non-polymers00
Water17,060947
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.246, 94.498, 75.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MALONAMIDASE E2


Mass: 43677.645 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRADYRHIZOBIUM JAPONICUM (bacteria) / Plasmid: PUC18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZIV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 947 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCIS PEPTIDE BOND BETWEEN GLYCINE 130 AND SERINE 131 ENGINEERED RESIDUE LYS (62) ALA

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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 Å3/Da / Density % sol: 39.9 %
Crystal growpH: 7 / Details: 20% POLYETHYLENE GLYCOL 1000, 100 MM TRIS, PH 7.0
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 %PEG10001reservoir
30.1 MTris-HCl1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 50620 / % possible obs: 89 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rsym value: 0.069 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.217 / % possible all: 76.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. measured all: 384083 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 76.1 % / Rmerge(I) obs: 0.217

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GR8

1gr8
PDB Unreleased entry


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.23 -5 %RANDOM
Rwork0.173 ---
obs0.173 44975 89 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6118 0 0 947 7065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0051
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.258
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEP.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0032
X-RAY DIFFRACTIONc_angle_deg1.034

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