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- PDB-2hxv: Crystal structure of a diaminohydroxyphosphoribosylaminopyrimidin... -

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Entry
Database: PDB / ID: 2hxv
TitleCrystal structure of a diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase (tm1828) from thermotoga maritima at 1.80 A resolution
ComponentsDiaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase
KeywordsBIOSYNTHETIC PROTEIN / Oxidoreductase / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / nucleotide binding / zinc ion binding
Similarity search - Function
Riboflavin biosynthesis protein RibD / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. ...Riboflavin biosynthesis protein RibD / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Riboflavin biosynthesis protein RibD
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase (TM1828) from Thermotoga maritima at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,25112
Polymers40,6681
Non-polymers1,58311
Water3,693205
1
A: Diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase
hetero molecules

A: Diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,50124
Polymers81,3352
Non-polymers3,16622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10910 Å2
ΔGint-149 kcal/mol
Surface area27470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.180, 104.180, 145.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase


Mass: 40667.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1828 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X2E8, diaminohydroxyphosphoribosylaminopyrimidine deaminase, 5-amino-6-(5-phosphoribosylamino)uracil reductase

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Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3447.06
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop7.55.0% PEG-3000, 10.0% Glycerol, 30.0% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop7.55.0% PEG-3000, 10.0% Glycerol, 30.0% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.000001
SYNCHROTRONSSRL BL11-120.979170, 0.918370, 0.978913
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0000011
20.979171
30.918371
40.9789131
ReflectionResolution: 1.8→28.341 Å / Num. obs: 37367 / % possible obs: 99.7 % / Redundancy: 4.945 % / Biso Wilson estimate: 30.526 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.8-1.863.7110.7191.7122207593897.7
1.86-1.940.5062.626451703192
1.94-2.030.3753.525888685795
2.03-2.130.3194.828217642396.7
2.13-2.270.23735038727597.3
2.27-2.440.1799.637652681698.7
2.44-2.690.1313.442415716899.1
2.69-3.070.0820.640986693799.4
3.070.0433542101717699.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→28.341 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.664 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. NADPH WAS MODELED BASED ON DENSITY AND PROPOSED FUNCTION. 5. ZN METAL IDENTIFICATION SUPPORTED BY EXCITATION AND FLOURESENCE SCAN ANALYSIS, IN ADDITION TO GEOMETRY AND HOMOLOGS. 6.GLYCEROL AND CL WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 7. RESIDUES 80-81 WERE MODELED IN VERY WEAK DENSITY. 8. UNKNOWN DENSITIES NEAR LYS 14 AND LYS 304 WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1877 5 %RANDOM
Rwork0.16 ---
obs0.162 37365 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 98 205 3000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222873
X-RAY DIFFRACTIONr_bond_other_d0.0010.022639
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9943895
X-RAY DIFFRACTIONr_angle_other_deg0.99936124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67623.388121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04415466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4741519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02576
X-RAY DIFFRACTIONr_nbd_refined0.2090.2544
X-RAY DIFFRACTIONr_nbd_other0.190.22786
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21445
X-RAY DIFFRACTIONr_nbtor_other0.0870.21766
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.219
X-RAY DIFFRACTIONr_mcbond_it2.41531796
X-RAY DIFFRACTIONr_mcbond_other0.6413716
X-RAY DIFFRACTIONr_mcangle_it3.35352840
X-RAY DIFFRACTIONr_scbond_it5.47381197
X-RAY DIFFRACTIONr_scangle_it7.869111050
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 127 -
Rwork0.217 2536 -
obs-2663 98.7 %
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)
10.84571.0195-0.00243.0063-0.17630.1820.03250.02150.04840.0132-0.02560.1208-0.0016-0.0261-0.0069-0.058-0.0005-0.0073-0.0883-0.0178-0.068926.527-3.03322.838
20.3364-0.05520.41150.1889-0.3371.4062-0.02920.01370.01510.0058-0.0261-0.0041-0.06040.12780.0554-0.0985-0.0220.0021-0.0686-0.0175-0.060537.2727.88815.955
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11-3 - 1469 - 158
22147 - 345159 - 357

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