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- PDB-4dzh: Crystal structure of an adenosine deaminase from xanthomonas camp... -

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Basic information

Entry
Database: PDB / ID: 4dzh
TitleCrystal structure of an adenosine deaminase from xanthomonas campestris (target nysgrc-200456) with bound zn
ComponentsAMIDOHYDROLASE
KeywordsHYDROLASE / Amidohydrolase / Adenosine deaminase / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / TIM-barrel structural fold. PSI-Biology
Function / homology
Function and homology information


5'-methylthioadenosine deaminase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / 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
Unknown ligand / Amidohydro-rel domain-containing protein
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 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 xanthomonas campestris (target nysgrc-200456) 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
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 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_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_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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8928
Polymers51,4871
Non-polymers4057
Water4,450247
1
A: AMIDOHYDROLASE
hetero molecules

A: AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,78416
Polymers102,9752
Non-polymers80914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7770 Å2
ΔGint-261 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.645, 53.150, 67.390
Angle α, β, γ (deg.)90.00, 106.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

21A-611-

HOH

Detailsbiological unit is a dimer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein AMIDOHYDROLASE


Mass: 51487.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: ATCC 33913 / Gene: XCC2270 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8P8H1

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 7
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM MgCl); Reservoir (1.0 M Succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% Peg MME 2000); Cryoprotection (Reservoir, + 20% glycerol + ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM MgCl); Reservoir (1.0 M Succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% Peg MME 2000); Cryoprotection (Reservoir, + 20% glycerol + 10 mM ZnCl, 10 mM Inosine), sitting drop vapor diffuction, temperature 298K

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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: Jul 27, 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: 1.55→40 Å / Num. all: 65349 / Num. obs: 65349 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 17.59 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 18.9
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6504 / Rsym value: 0.527 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
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: 1.552→17.968 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.7964 / SU ML: 0.19 / σ(F): 0 / σ(I): 0 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 3314 5.07 %RANDOM
Rwork0.2082 ---
all0.2095 65346 --
obs0.2095 65346 99.48 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.813 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso max: 73.79 Å2 / Biso mean: 26.2804 Å2 / Biso min: 10.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.3974 Å20 Å25.0132 Å2
2---0.2672 Å2-0 Å2
3----0.1302 Å2
Refinement stepCycle: LAST / Resolution: 1.552→17.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 20 247 3600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0243519
X-RAY DIFFRACTIONf_angle_d1.5084834
X-RAY DIFFRACTIONf_chiral_restr0.105556
X-RAY DIFFRACTIONf_plane_restr0.008635
X-RAY DIFFRACTIONf_dihedral_angle_d13.1081258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5517-1.57380.36791050.31622476258195
1.5738-1.59730.34181610.315325912752100
1.5973-1.62230.32881300.29825602690100
1.6223-1.64880.29311290.28125912720100
1.6488-1.67720.34181400.275626092749100
1.6772-1.70770.3041230.270225972720100
1.7077-1.74050.27931420.256725512693100
1.7405-1.7760.311590.260825632722100
1.776-1.81460.29441290.258325882717100
1.8146-1.85680.31611380.249826102748100
1.8568-1.90320.27851540.249325792733100
1.9032-1.95460.25481320.239325852717100
1.9546-2.0120.28281450.238225762721100
2.012-2.07690.27391370.231525642701100
2.0769-2.1510.24321500.224125952745100
2.151-2.23690.25321380.21426082746100
2.2369-2.33850.2511320.212626072739100
2.3385-2.46150.24461420.201525982740100
2.4615-2.61530.22211440.208725772721100
2.6153-2.81660.25241370.206526362773100
2.8166-3.09870.20391440.200125872731100
3.0987-3.54410.20551310.176726532784100
3.5441-4.45390.16451390.15722618275799
4.4539-17.96920.18141330.17572513264693
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)
11.3874-0.589-0.45510.4187-0.22581.1547-0.16050.19870.0285-0.0446-0.04270.02220.2498-0.28490.05780.121-0.1069-0.00250.1798-0.0831-0.0297-2.863621.768218.1936
21.5723-0.0499-0.46950.47130.20660.5382-0.10470.23220.5468-0.02340.2712-0.27910.14880.11590.0182-0.0263-0.15050.08-0.14750.13040.06624.846732.775121.304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:112)A9 - 112
2X-RAY DIFFRACTION2chain 'A' and (resseq 113:447)A113 - 447

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