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- PDB-1ock: THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM -

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Basic information

Entry
Database: PDB / ID: 1ock
TitleTHE CRYSTAL STRUCTURE OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM
ComponentsMALONAMIDASE E2
KeywordsAMIDASE / MALONAMIDASE
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 / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsShin, S. / Ha, N.-C. / Lee, T.-H. / 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
DepositionFeb 8, 2003Deposition site: PDBE / Processing site: PDBE
SupersessionMar 3, 2003ID: 1GR8
Revision 1.0Mar 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _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)87,1832
Polymers87,1832
Non-polymers00
Water16,916939
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.287, 95.581, 74.899
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: 43591.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CIS PEPTIDE BOND BETWEEN GLY 130 AND SER 131 / Source: (gene. exp.) BRADYRHIZOBIUM JAPONICUM (bacteria) / Plasmid: PUC18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AD494(DE3) / References: UniProt: Q9ZIV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYZES MALONAMATE (-OOCCH2CONH2) INTO MALONATE AND AMMONIA. INVOLVED IN THE TRANSPORT OF FIXED ...HYDROLYZES MALONAMATE (-OOCCH2CONH2) INTO MALONATE AND AMMONIA. INVOLVED IN THE TRANSPORT OF FIXED NITROGEN FROM BACTEROIDS TO PLANT CELLS IN SYMBIOTIC NITROGEN METABOLISM
Sequence detailsTHE RESIDUES 401-412 DIFFER FROM THAT IN THE SWISS-PROT ENTRY Q9ZIV5 DUE TO FRAME SHIFT BECAUSE OF ...THE RESIDUES 401-412 DIFFER FROM THAT IN THE SWISS-PROT ENTRY Q9ZIV5 DUE TO FRAME SHIFT BECAUSE OF ADDITION OF ADENINE 1202 IN THE ORIGINAL SEQUENCE.

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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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 68327 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.037 / Net I/σ(I): 41.76
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Mean I/σ(I) obs: 9.81 / Rsym value: 0.113 / % possible all: 93.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / Rfactor Rfree error: 6.5E-5 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3477 5 %RANDOM
Rwork0.19 ---
obs0.19 68274 97.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.755 Å20 Å20 Å2
2---5.201 Å20 Å2
3---0.446 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 0 939 7065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0049
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_deg1.276
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

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