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- PDB-4aib: Crystal Structure of Ornithine Decarboxylase from Entamoeba histo... -

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Basic information

Entry
Database: PDB / ID: 4aib
TitleCrystal Structure of Ornithine Decarboxylase from Entamoeba histolytica.
ComponentsORNITHINE DECARBOXYLASE
KeywordsLYASE
Function / homology
Function and homology information


putrescine biosynthetic process from ornithine / ornithine decarboxylase / ornithine decarboxylase activity / cytoplasm
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ornithine decarboxylase
Similarity search - Component
Biological speciesENTAMOEBA HISTOLYTICA (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsPreeti, P. / Kumar, P. / Tomar, S.
CitationJournal: Plos One / Year: 2013
Title: Structural Insight Into Dfmo Resistant Ornithine Decarboxylase from Entamoeba Histolytica: An Inkling to Adaptive Evolution.
Authors: Preeti, P. / Tapas, S. / Kumar, P. / Tomar, S.
History
DepositionFeb 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORNITHINE DECARBOXYLASE
B: ORNITHINE DECARBOXYLASE
C: ORNITHINE DECARBOXYLASE
D: ORNITHINE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)178,2994
Polymers178,2994
Non-polymers00
Water1,820101
1
A: ORNITHINE DECARBOXYLASE
B: ORNITHINE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)89,1502
Polymers89,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-8.8 kcal/mol
Surface area30780 Å2
MethodPISA
2
C: ORNITHINE DECARBOXYLASE
D: ORNITHINE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)89,1502
Polymers89,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-6 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.671, 119.283, 179.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ORNITHINE DECARBOXYLASE /


Mass: 44574.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTAMOEBA HISTOLYTICA (eukaryote) / Strain: HM-1\:IMSS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58P26, ornithine decarboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.28 Å3/Da / Density % sol: 46.02 % / Description: NONE
Crystal growDetails: POLYETHYLENE GLYCOL, LITHIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 15, 2011 / Details: HELIOS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.87→100 Å / Num. obs: 35570 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.82
Reflection shellResolution: 2.87→2.92 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 59

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ON3

2on3


Resolution: 2.87→99.5 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.861 / SU B: 25.851 / SU ML: 0.451 / Cross valid method: THROUGHOUT / ESU R: 2.077 / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29934 1763 5 %RANDOM
Rwork0.25266 ---
obs0.253 33646 91.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.427 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2--1.21 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.87→99.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10484 0 0 101 10585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0210701
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8311.96714423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.76351289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19825.195487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.866151954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.8711536
X-RAY DIFFRACTIONr_chiral_restr0.0560.21596
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217942
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.866→2.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 58 -
Rwork0.434 1540 -
obs--59.14 %

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