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- PDB-2a3l: X-Ray Structure of Adenosine 5'-Monophosphate Deaminase from Arab... -

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Basic information

Entry
Database: PDB / ID: 2a3l
TitleX-Ray Structure of Adenosine 5'-Monophosphate Deaminase from Arabidopsis Thaliana in Complex with Coformycin 5'-Phosphate
ComponentsAMP deaminase
KeywordsHYDROLASE / ATAMPD / At2g38280 / ADENOSINE 5'-MONOPHOSPHATE DEAMINASE / coformycin 5'-phosphate / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


AMP deaminase / AMP deaminase activity / : / IMP biosynthetic process / AMP metabolic process / protein histidine kinase binding / embryo development ending in seed dormancy / IMP salvage / response to abscisic acid / intracellular membrane-bounded organelle ...AMP deaminase / AMP deaminase activity / : / IMP biosynthetic process / AMP metabolic process / protein histidine kinase binding / embryo development ending in seed dormancy / IMP salvage / response to abscisic acid / intracellular membrane-bounded organelle / endoplasmic reticulum / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Invariant Chain; Chain I - #20 / AMP deaminase / Invariant Chain; Chain I / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / Few Secondary Structures ...Invariant Chain; Chain I - #20 / AMP deaminase / Invariant Chain; Chain I / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / Few Secondary Structures / Irregular / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
COFORMYCIN 5'-PHOSPHATE / PHOSPHATE ION / AMP deaminase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.34 Å
AuthorsHan, B.W. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1).
Authors: Han, B.W. / Bingman, C.A. / Mahnke, D.K. / Bannen, R.M. / Bednarek, S.Y. / Sabina, R.L. / Phillips, G.N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and preliminary X-ray crystallographic analysis of adenosine 5'-monophosphate deaminase (AMPD) from Arabidopsis thaliana in complex with coformycin 5'-phosphate
Authors: Han, B.W. / Bingham, C.A. / Mahnke, D.K. / Sabina, R.L. / Phillips Jr., G.N.
History
DepositionJun 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9344
Polymers80,4101
Non-polymers5253
Water43224
1
A: AMP deaminase
hetero molecules

A: AMP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,8698
Polymers160,8202
Non-polymers1,0496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area7310 Å2
ΔGint-130 kcal/mol
Surface area47640 Å2
MethodPISA, PQS
2
A: AMP deaminase
hetero molecules

A: AMP deaminase
hetero molecules

A: AMP deaminase
hetero molecules

A: AMP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,73816
Polymers321,6394
Non-polymers2,09912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_444-y-1,-x-1,-z-1/31
Buried area17510 Å2
ΔGint-288 kcal/mol
Surface area92380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.325, 131.325, 208.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein AMP deaminase / AMPD


Mass: 80409.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g38280 / Plasmid: P2BAC / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O80452
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CF5 / COFORMYCIN 5'-PHOSPHATE


Mass: 364.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N4O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 295 K / pH: 5.6
Details: 8 MG/ML PROTEIN, 0.40 M MONOAMMONIUM DIHYDROGEN PHOSPHATE, 0.10 M TRI-SODIUM CITRATE, 10% (V/V) ETHANOL, vapor diffusion, hanging drop, temperature 295K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97931
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionRedundancy: 6.1 % / Number: 16001 / Rmerge(I) obs: 0.06 / Χ2: 1.071 / D res high: 3.34 Å / D res low: 50 Å / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.235098.410.0220.8815.4
6.538.2399.810.0290.9356
5.716.5310010.040.9996.2
5.195.7110010.0471.0146.2
4.825.1999.610.0491.1056.2
4.534.8299.410.0571.1426.3
4.314.5399.210.0711.2436.2
4.124.3199.210.0921.236.3
3.964.1299.810.1181.156.3
3.823.9610010.1541.1336.4
3.73.8299.910.1851.0736.4
3.63.799.910.2521.0536.4
3.53.610010.3331.0726.3
3.423.599.910.3890.9965.9
3.343.4299.510.4891.0135.7
ReflectionResolution: 3.34→50 Å / Num. obs: 16001 / % possible obs: 99.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.579
Reflection shellResolution: 3.34→3.42 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.922 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å47.88 Å
Translation3 Å47.88 Å

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
SCALEPACKdata scaling
MOLREPphasing
REFMAC1.1refinement
PDB_EXTRACT1.6data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RABBIT AMPD

Resolution: 3.34→49.91 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 273226 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.323 741 4.9 %RANDOM
Rwork0.237 ---
obs0.237 15038 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.73 Å2 / ksol: 0.272 e/Å3
Displacement parametersBiso mean: 73.5 Å2
Baniso -1Baniso -2Baniso -3
1-10.914 Å2-1.407 Å20 Å2
2--10.914 Å20 Å2
3----21.828 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.34→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 30 24 5104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
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_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.48
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
LS refinement shellResolution: 3.34→3.55 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 116 5.2 %
Rwork0.297 2094 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMprotein.top
X-RAY DIFFRACTION2CF5.PARwater.top
X-RAY DIFFRACTION3PO4.PARCF5.top
X-RAY DIFFRACTION4ZN.PARPO4.top
X-RAY DIFFRACTION5CNS_TOPPAR:WATER_REP.PARAMZN.top

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