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- PDB-3tc3: Crystal Structure of SacUVDE -

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Basic information

Entry
Database: PDB / ID: 3tc3
TitleCrystal Structure of SacUVDE
ComponentsUV damage endonuclease
KeywordsHYDROLASE / TIM-barrel / endonuclease
Function / homology
Function and homology information


Hydrolases / response to UV / nucleotide-excision repair / endonuclease activity / metal ion binding
Similarity search - Function
UV-endonuclease UvdE / UV-endonuclease UvdE / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / UV damage endonuclease
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMeulenbroek, E.M. / Jala, I. / Moolenaar, G.F. / Goosen, N. / Pannu, N.S.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: UV damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different DNA lesions.
Authors: Meulenbroek, E.M. / Peron Cane, C. / Jala, I. / Iwai, S. / Moolenaar, G.F. / Goosen, N. / Pannu, N.S.
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Feb 6, 2013Group: Database references
Revision 1.4Sep 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_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.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_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: UV damage endonuclease
B: UV damage endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5074
Polymers71,3982
Non-polymers1102
Water10,395577
1
A: UV damage endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7542
Polymers35,6991
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UV damage endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7542
Polymers35,6991
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.075, 53.585, 77.395
Angle α, β, γ (deg.)102.10, 93.02, 111.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein UV damage endonuclease


Mass: 35698.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: uvdE, Saci_1096 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9T1, Hydrolases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 20 % PEG3350, 0.25 M NH4Cl, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.5→46.05 Å / Num. all: 94666 / Num. obs: 94666 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 9.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / Num. unique all: 13351 / Rsym value: 0.52 / % possible all: 94

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.6.0116refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2j6v

2j6v


Resolution: 1.5→46.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.826 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21395 4732 5 %RANDOM
Rwork0.17728 ---
obs0.1791 89933 97.27 %-
all-89933 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20.05 Å20.66 Å2
2--0.17 Å20.27 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 2 577 5245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224799
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.9616478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1424.578225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27115940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1871530
X-RAY DIFFRACTIONr_chiral_restr0.1580.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213526
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 338 -
Rwork0.331 6333 -
obs-6333 93.61 %
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)
11.14280.5765-0.15590.87470.12570.21630.0597-0.05490.01560.0646-0.06010.03750.00330.02020.00040.02490.0038-0.01330.03760.00130.02236.11435.96636.959
20.6551-0.1393-0.33290.76830.26410.59220.03120.03420.014-0.0564-0.0146-0.0294-0.0483-0.0248-0.01660.03040.0104-0.0070.04840.01430.011118.3830.08474.533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 288
2X-RAY DIFFRACTION2B0 - 289

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