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- PDB-2awp: Crystal structure of Plasmodium knowlesi structure of Iron Super-... -

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Basic information

Entry
Database: PDB / ID: 2awp
TitleCrystal structure of Plasmodium knowlesi structure of Iron Super-Oxide Dismutase
ComponentsIron Super-Oxide Dismutase
KeywordsOXIDOREDUCTASE / Iron Super-Oxide Dismutase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
Superoxide dismutase
Similarity search - Component
Biological speciesPlasmodium knowlesi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Vedadi, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Vedadi, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionSep 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Remark 300 BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ... BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS STATE THE BIOLOGICAL UNIT IS UNKNOWN.
Remark 999 SEQEUNCE THE PLASMODIUM KNOWLESI IRON SUPEROXIDE DISMUTASE SEQUENCE COMES FROM THE SANGER INSTITUTE WEBSITE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron Super-Oxide Dismutase
B: Iron Super-Oxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4947
Polymers45,4232
Non-polymers715
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-29 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.240, 79.053, 88.672
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 Iron Super-Oxide Dismutase


Mass: 22711.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: D0VWV6*PLUS, superoxide dismutase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 5.1
Details: 30%PEG4K,0.2M NH4 Acetate,0.1M Na Cacodylate,5mM MnCl2, pH 5.1, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 5, 2005 / Details: VeriMax
RadiationMonochromator: VeriMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 26770 / Num. obs: 26770 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/σ(I): 4.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.43 / Rsym value: 0.578 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AO3

2ao3
PDB Unreleased entry


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.712 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1091 4.1 %RANDOM
Rwork0.15817 ---
obs0.1609 25638 99.45 %-
all-25638 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.707 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.94 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 5 559 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213277
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9064456
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9825.385169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43415523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.586154
X-RAY DIFFRACTIONr_chiral_restr0.1020.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21723
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22244
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2404
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7851.52001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25223126
X-RAY DIFFRACTIONr_scbond_it2.07731516
X-RAY DIFFRACTIONr_scangle_it3.114.51330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 97 -
Rwork0.18 1839 -
obs--97.88 %

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