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- PDB-2ood: Crystal structure of guanine deaminase from Bradyrhizobium japonicum -

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Basic information

Entry
Database: PDB / ID: 2ood
TitleCrystal structure of guanine deaminase from Bradyrhizobium japonicum
ComponentsBlr3880 protein
KeywordsHYDROLASE / PSI-II / PSI-2 / 9231a / guanine deaminase / guanine / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


guanine deaminase / guanine deaminase activity / guanine catabolic process / deaminase activity / guanine metabolic process / zinc ion binding
Similarity search - Function
Guanine deaminase / 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 ...Guanine deaminase / 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
GUANINE / Guanine deaminase
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.62 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of guanine deaminase from Bradyrhizobium japonicum
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Blr3880 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5703
Polymers53,3531
Non-polymers2172
Water5,585310
1
A: Blr3880 protein
hetero molecules

A: Blr3880 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1406
Polymers106,7072
Non-polymers4334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area6150 Å2
ΔGint-97 kcal/mol
Surface area29320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)193.216, 193.216, 121.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Blr3880 protein / Guanine deaminase


Mass: 53353.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bII3846, blr3880 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus RIL / References: UniProt: Q89NG0, guanine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 1.4 M Sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2007 / Details: mirrors
RadiationMonochromator: si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. all: 36811 / Num. obs: 36811 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 35.3 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.5
Reflection shellResolution: 2.62→2.71 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1 / Num. unique all: 2158 / % possible all: 53.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.62→41.09 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 36133.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: 1. THE RESIDUES LISTED AS MISSING IN REMARK 465 ARE DUE TO LACK OR ABSENCE OF ELECTRON DENSITY. 2. AUTHORS HAVE MODELED THE RESIDUAL DENSITY AS THE SUBSTRATE GUANINE AT THE ACTIVE SITE. IT ...Details: 1. THE RESIDUES LISTED AS MISSING IN REMARK 465 ARE DUE TO LACK OR ABSENCE OF ELECTRON DENSITY. 2. AUTHORS HAVE MODELED THE RESIDUAL DENSITY AS THE SUBSTRATE GUANINE AT THE ACTIVE SITE. IT COULD AS WELL BE XANTHINE, THE PRODUCT OF CATALYTIC REACTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 1043 3 %RANDOM
Rwork0.1865 ---
all0.22 36811 --
obs0.1865 34927 86.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.589 Å2 / ksol: 0.332391 e/Å3
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-12.978 Å21.286 Å20 Å2
2--12.978 Å20 Å2
3----25.956 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.62→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 12 310 3939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.62→2.78 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 130 3.5 %
Rwork0.281 3566 -
obs-36811 55.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4gun.paramgun.top

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