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- PDB-3l0a: Crystal structure of Putative exonuclease (RER070207002219) from ... -

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Basic information

Entry
Database: PDB / ID: 3l0a
TitleCrystal structure of Putative exonuclease (RER070207002219) from Eubacterium rectale at 2.19 A resolution
ComponentsPutative exonuclease
KeywordsHYDROLASE / RER070207002219 / Putative exonuclease / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Putative exodeoxyribonuclease 8, PDDEXK-like domain / PDDEXK-like domain of unknown function (DUF3799) / Lambda Exonuclease; Chain A - #10 / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative exodeoxyribonuclease 8 PDDEXK-like domain-containing protein
Similarity search - Component
Biological speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative exonuclease (RER070207002219) from Eubacterium rectale at 2.19 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 1.4Feb 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9284
Polymers31,3861
Non-polymers5423
Water1,65792
1
A: Putative exonuclease
hetero molecules

A: Putative exonuclease
hetero molecules

A: Putative exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,78412
Polymers94,1583
Non-polymers1,6269
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7390 Å2
ΔGint-4 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.248, 88.248, 69.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TRIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative exonuclease


Mass: 31385.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Strain: ATCC 33656 / VPI 0990 / Gene: EUBREC_2131, RER070207002219 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: C4ZCC6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M MgCl2, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97936,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979361
30.979221
ReflectionResolution: 2.19→44.108 Å / Num. obs: 15931 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 54.969 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.19-2.270.5762728316081100
2.27-2.360.5723.41273215601100
2.36-2.470.4454.31324616231100
2.47-2.60.2966.21280815671100
2.6-2.760.238.61341215611100
2.76-2.970.21312.9177471564199.9
2.97-3.270.13420.2200311614199.9
3.27-3.740.06931.91940015831100
3.74-4.70.0541.51914315941100
4.7-44.1080.04745.8189841658199.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.19→44.108 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.408 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.216
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. A ZINC ION HAS BEEN MODELED BASED ON THE CHEMICAL ENVIRONMENT AND ANOMALOUS DIFFERENCE FOURIERS. 5. PEG-4000 FRAGMENT (PE4) AND TROMETHAMINE (TRS) MOLECULE FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 793 5 %RANDOM
Rwork0.208 ---
obs0.21 15916 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 103.25 Å2 / Biso mean: 26.641 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-4.32 Å22.16 Å20 Å2
2--4.32 Å20 Å2
3----6.48 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 25 92 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222216
X-RAY DIFFRACTIONr_bond_other_d0.0010.021539
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9682986
X-RAY DIFFRACTIONr_angle_other_deg0.9333748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9885273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35324.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09815398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7781512
X-RAY DIFFRACTIONr_chiral_restr0.0920.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_mcbond_it0.7281.51334
X-RAY DIFFRACTIONr_mcbond_other0.1541.5547
X-RAY DIFFRACTIONr_mcangle_it1.34222145
X-RAY DIFFRACTIONr_scbond_it2.2643882
X-RAY DIFFRACTIONr_scangle_it3.4224.5837
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 60 -
Rwork0.278 1117 -
all-1177 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 9.661 Å / Origin y: 28.277 Å / Origin z: 42.847 Å
111213212223313233
T0.1724 Å20.0666 Å2-0.0252 Å2-0.219 Å20.0317 Å2--0.4834 Å2
L2.2459 °20.1111 °2-0.4269 °2-0.0464 °20.1954 °2--1.2091 °2
S0.0001 Å °-0.0246 Å °-0.3791 Å °0.0938 Å °0.0084 Å °0.0208 Å °0.4052 Å °0.209 Å °-0.0086 Å °

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