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- PDB-2ewo: X-ray structure of putative agmatine deiminase Q8DW17, Northeast ... -

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Basic information

Entry
Database: PDB / ID: 2ewo
TitleX-ray structure of putative agmatine deiminase Q8DW17, Northeast Structural Genomics target SmR6.
ComponentsPutative agmatine deiminase
KeywordsHYDROLASE / Q8DW17 / SmR6 / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


agmatine deiminase / agmatine deiminase activity / putrescine biosynthetic process / protein-arginine deiminase activity
Similarity search - Function
Agmatine deiminase / Peptidyl-arginine deiminase, Porphyromonas-type / Porphyromonas-type peptidyl-arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
Putative agmatine deiminase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsKuzin, A.P. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: X-ray structure of putative agmatine deiminase Q8DW17, Northeast Structural Genomics target SmR6.
Authors: Kuzin, A.P. / Chen, Y. / Vorobiev, S.M. / Su, M. / Forouhar, F. / Acton, T. / Xiao, R. / Conover, K. / Ma, L.-C. / Kellie, R. / Cunningham, K.E. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionNov 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative agmatine deiminase
B: Putative agmatine deiminase
C: Putative agmatine deiminase
D: Putative agmatine deiminase
E: Putative agmatine deiminase
F: Putative agmatine deiminase
G: Putative agmatine deiminase
H: Putative agmatine deiminase
I: Putative agmatine deiminase
J: Putative agmatine deiminase
K: Putative agmatine deiminase
L: Putative agmatine deiminase


Theoretical massNumber of molelcules
Total (without water)519,96712
Polymers519,96712
Non-polymers00
Water4,035224
1
A: Putative agmatine deiminase
B: Putative agmatine deiminase
F: Putative agmatine deiminase
G: Putative agmatine deiminase


Theoretical massNumber of molelcules
Total (without water)173,3224
Polymers173,3224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-37 kcal/mol
Surface area51390 Å2
MethodPISA
2
C: Putative agmatine deiminase
D: Putative agmatine deiminase
I: Putative agmatine deiminase
J: Putative agmatine deiminase


Theoretical massNumber of molelcules
Total (without water)173,3224
Polymers173,3224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-36 kcal/mol
Surface area51440 Å2
MethodPISA
3
E: Putative agmatine deiminase
H: Putative agmatine deiminase
K: Putative agmatine deiminase
L: Putative agmatine deiminase


Theoretical massNumber of molelcules
Total (without water)173,3224
Polymers173,3224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-36 kcal/mol
Surface area52090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.524, 203.685, 139.543
Angle α, β, γ (deg.)90.00, 104.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative agmatine deiminase / Agmatine iminohydrolase


Mass: 43330.594 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: aguA / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8DW17, agmatine deiminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Description: THE STRUCTURE FACTOR FILE contians FRIEDEL PAIRS.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 16% PEG6K, 100mM Tris-HCl, 400mM LiCl, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97938 0.97952 0.96793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 25, 2005 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979381
20.979521
30.967931
ReflectionResolution: 2.8→30 Å / Num. obs: 218714 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.99

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→19.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 182654.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The toatal number of unique reflections is 437428. There are 218714 of Friedel pairs. But only 182596 reflections was used for resolution range 20.0A -2.9A, for F > 2sigmaF.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 8931 4.9 %RANDOM
Rwork0.235 ---
obs0.235 182581 83.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.265542 e/Å3
Displacement parametersBiso mean: 46.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.62 Å20 Å2-0.38 Å2
2--4.04 Å20 Å2
3---2.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34710 0 0 224 34934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.4
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 1002 4.8 %
Rwork0.336 19906 -
obs--57.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4PARM_HOME:acy.parPARM_HOME:acy.top

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