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Basic information

Entry
Database: PDB / ID: 4dyk
TitleCrystal structure of an adenosine deaminase from pseudomonas aeruginosa pao1 (target nysgrc-200449) with bound zn
ComponentsAMIDOHYDROLASE
KeywordsHYDROLASE / Amidohydrolase / Adenosine deaminase / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


5'-methylthioadenosine deaminase activity / adenosine deaminase activity / metal ion binding
Similarity search - Function
Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel ...Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Amidohydrolase-related domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Chamala, S. / Kar, A. / Lafleur, J. / Villigas, G. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Chamala, S. / Kar, A. / Lafleur, J. / Villigas, G. / Evans, B. / Hammonds, J. / Gizzi, A. / Zencheck, W.D. / Hillerich, B. / Love, J. / Seidel, R.D. / Bonanno, J.B. / Raushel, F.M. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of an adenosine deaminase from pseudomonas aeruginosa pao1 (target nysgrc-200449) with bound zn
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Chamala, S. / Kar, A. / Lafleur, J. / Villigas, G. / Evans, B. / Hammonds, J. / Gizzi, A. / Zencheck, ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Chamala, S. / Kar, A. / Lafleur, J. / Villigas, G. / Evans, B. / Hammonds, J. / Gizzi, A. / Zencheck, W.D. / Hillerich, B. / Love, J. / Seidel, R.D. / Bonanno, J.B. / Raushel, F.M. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMIDOHYDROLASE
B: AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2889
Polymers98,8322
Non-polymers4567
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-129 kcal/mol
Surface area29650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.906, 98.776, 119.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a dimer

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Components

#1: Protein AMIDOHYDROLASE


Mass: 49416.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3170 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HZ64
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol); Reservoir (0.2 M MgCl, 0.1M Bis-Tris pH 6.5, 25% Peg3350); Cryoprotection (Reservoir, + 20% glycerol), sitting drop vapor ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol); Reservoir (0.2 M MgCl, 0.1M Bis-Tris pH 6.5, 25% Peg3350); Cryoprotection (Reservoir, + 20% glycerol), sitting drop vapor diffuction, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 20, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 59764 / Num. obs: 59764 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.068 / Χ2: 1.576 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.034.70.75328921.212198.9
2.03-2.074.80.67729621.257199.2
2.07-2.114.80.53629011.201198.8
2.11-2.154.80.50629461.22199.7
2.15-2.24.90.43129621.246199.3
2.2-2.254.90.35429561.277199.9
2.25-2.3150.30629651.248199.6
2.31-2.375.10.2529531.251199.8
2.37-2.445.10.22629591.263199.9
2.44-2.525.20.18629921.272199.9
2.52-2.615.20.14629861.253199.9
2.61-2.715.30.12329681.2951100
2.71-2.845.40.11129821.4991100
2.84-2.995.40.10430111.828199.9
2.99-3.175.50.0929962.245199.8
3.17-3.425.50.07330102.519199.7
3.42-3.765.50.06230162.844199.9
3.76-4.315.70.04430532.127199.9
4.31-5.435.70.03230771.6199.9
5.43-505.30.02531771.293198

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3LNP

3lnp


Resolution: 2→31.748 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8405 / SU ML: 0.18 / σ(F): 0 / σ(I): 0 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 1870 3.35 %RANDOM
Rwork0.1759 ---
all0.1774 55862 --
obs0.1774 55862 93.04 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.771 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 124.24 Å2 / Biso mean: 45.3523 Å2 / Biso min: 18.61 Å2
Baniso -1Baniso -2Baniso -3
1--8.147 Å20 Å20 Å2
2--2.21 Å20 Å2
3---5.937 Å2
Refinement stepCycle: LAST / Resolution: 2→31.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6704 0 22 309 7035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086883
X-RAY DIFFRACTIONf_angle_d1.1039375
X-RAY DIFFRACTIONf_chiral_restr0.0761050
X-RAY DIFFRACTIONf_plane_restr0.0051234
X-RAY DIFFRACTIONf_dihedral_angle_d14.1992504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9988-2.05290.35391240.27693485360979
2.0529-2.11320.32121360.24893755389186
2.1132-2.18140.27681360.22823838397487
2.1814-2.25940.24071390.20583954409390
2.2594-2.34980.24151360.18894073420992
2.3498-2.45670.2311410.19414082422392
2.4567-2.58620.25091470.19124177432494
2.5862-2.74810.23021420.18754276441896
2.7481-2.96020.25661470.19534322446997
2.9602-3.25780.23821490.19264367451698
3.2578-3.72860.20681550.16694465462099
3.7286-4.69520.18921560.134845314687100
4.6952-31.75250.19461620.16084667482999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9804-0.0068-0.1340.4747-0.40970.58330.0475-0.0455-0.228-0.02550.0258-0.3020.02460.2472-0.00090.2332-0.0433-0.03720.2795-0.01310.288741.664652.403164.8788
20.2470.08860.03740.2539-0.03770.0303-0.0279-0.1717-0.56860.00470.0556-0.29170.13630.14880.18810.31210.0772-0.15160.24130.21920.61441.344134.932574.1856
30.10570.0179-0.10430.19030.04150.1340.0461-0.2345-0.03280.17640.088-0.1195-0.05040.07380.020.3056-0.0372-0.09030.31880.08190.258934.41754.81579.8847
40.2754-0.15770.02080.11170.01840.04590.06490.12850.1514-0.077-0.0011-0.0131-0.1141-0.14690.02990.2837-0.0527-0.02660.29040.07360.155931.763359.291861.0501
50.077-0.02150.04220.22990.01640.04880.08310.1526-0.0444-0.17110.11060.34440.1033-0.45760.02750.3174-0.0376-0.17950.4930.10.35182.830855.362853.6241
60.17190.0894-0.05710.17780.03070.12810.0544-0.2532-0.06540.1220.04210.2997-0.089-0.1185-0.00030.35220.00460.03260.42020.12350.31686.936759.578387.0345
70.47280.65590.08551.00190.50731.7583-0.1344-0.2403-0.12330.3361-0.12440.43060.1153-0.4809-1.22030.2631-0.14660.17560.45050.38520.5578-2.712144.434388.5013
80.8477-0.0613-0.13510.25180.0190.42060.03780.0578-0.12790.00350.03770.2479-0.0232-0.18950.00090.2369-0.0557-0.06370.24810.1150.293810.839250.294771.3423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:200)A6 - 200
2X-RAY DIFFRACTION2chain 'A' and (resseq 201:318)A201 - 318
3X-RAY DIFFRACTION3chain 'A' and (resseq 319:389)A319 - 389
4X-RAY DIFFRACTION4chain 'A' and (resseq 390:442)A390 - 442
5X-RAY DIFFRACTION5chain 'B' and (resseq 6:74)B6 - 74
6X-RAY DIFFRACTION6chain 'B' and (resseq 75:166)B75 - 166
7X-RAY DIFFRACTION7chain 'B' and (resseq 167:263)B167 - 263
8X-RAY DIFFRACTION8chain 'B' and (resseq 264:442)B264 - 442

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