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- PDB-3bwv: Crystal structure of deoxyribonucleotidase-like protein (NP_76406... -

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Basic information

Entry
Database: PDB / ID: 3bwv
TitleCrystal structure of deoxyribonucleotidase-like protein (NP_764060.1) from Staphylococcus epidermidis ATCC 12228 at 1.55 A resolution
ComponentsPutative 5'(3')-deoxyribonucleotidase
KeywordsHYDROLASE / NP_764060.1 / deoxyribonucleotidase-like protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


deoxyribonucleotide catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / metal ion binding
Similarity search - Function
5'(3')-deoxyribonucleotidase / 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) / Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...5'(3')-deoxyribonucleotidase / 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) / Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative 5'(3')-deoxyribonucleotidase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of deoxyribonucleotidase-like protein (NP_764060.1) from Staphylococcus epidermidis ATCC 12228 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_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
Remark 999 SEQUENCE THE CONSTRUCT USED FOR REFINEMENT WAS EXPRESSED WITH A PURIFICATION TAG ... SEQUENCE THE CONSTRUCT USED FOR REFINEMENT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative 5'(3')-deoxyribonucleotidase
B: Putative 5'(3')-deoxyribonucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0286
Polymers42,9092
Non-polymers1204
Water3,261181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.310, 40.270, 55.310
Angle α, β, γ (deg.)71.930, 75.080, 83.620
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative 5'(3')-deoxyribonucleotidase


Mass: 21454.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: NP_764060.1, SE_0505 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q8CTG7, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.87 Å3/Da / Density % sol: 34.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 17.6% PEG 3350, 0.4M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97908, 0.97959
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 9, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979081
30.979591
ReflectionResolution: 1.54→29.235 Å / Num. obs: 43195 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.438 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 4.92
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.54-1.60.5291.261687578175.2
1.6-1.660.4341.570228058194
1.66-1.730.3511.871848134194.3
1.73-1.830.252.485029608194.8
1.83-1.940.1683.473228336194.9
1.94-2.090.1114.876468767195
2.09-2.30.0826.376388880195.6
2.3-2.630.077.473228785195.9
2.63-3.310.059969608857195.5
3.31-29.2350.04510.466508811194.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0066refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.55→29.235 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.605 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.095
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. MG AND CL MODELED BASED ON GEOMETRY AND CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2176 5 %RANDOM
Rwork0.182 ---
obs0.184 43194 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.268 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0.21 Å2-0.58 Å2
2---0.79 Å20.77 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 4 181 2885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222819
X-RAY DIFFRACTIONr_bond_other_d0.0030.021879
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9413832
X-RAY DIFFRACTIONr_angle_other_deg1.04434576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64724.167144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77215476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5931516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
X-RAY DIFFRACTIONr_mcbond_it1.0041.51698
X-RAY DIFFRACTIONr_mcbond_other0.3011.5680
X-RAY DIFFRACTIONr_mcangle_it1.74822748
X-RAY DIFFRACTIONr_scbond_it3.10531121
X-RAY DIFFRACTIONr_scangle_it4.8124.51074
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 124 -
Rwork0.294 2792 -
all-2916 -
obs--86.76 %
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)
12.6255-0.0568-0.20491.8546-0.50951.54020.0451-0.0373-0.2010.00310.04450.15240.0587-0.0611-0.0896-0.0429-0.0036-0.0008-0.0424-0.0058-0.063216.442519.057944.5968
2000000000000000-0.0237-0.0243-0.0392-0.0504-0.01170.003615.910615.28541.5251
32.1807-0.40270.15751.1639-0.57591.39430.0158-0.01690.0008-0.02870.03260.1476-0.0099-0.0384-0.0483-0.0012-0.00370.0035-0.0453-0.0102-0.038816.80935.187219.5333
40000000000000000.0290.0070.0345-0.0212-0.0936-0.071116.369538.476522.5175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1783 - 179
2X-RAY DIFFRACTION2AC3001
3X-RAY DIFFRACTION3BB3 - 1784 - 179
4X-RAY DIFFRACTION4BD3001

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