HEADER DNA BINDING PROTEIN 24-MAY-21 7OMK TITLE THE NMR STRUCTURE OF THE ZF-GRF DOMAINS FROM THE MOUSE ENDONUCLEASE TITLE 2 VIII-LIKE 3 (MNEIL3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE 8-LIKE 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA GLYCOSYLASE FPG2,DNA GLYCOSYLASE/AP LYASE NEIL3, COMPND 5 ENDONUCLEASE VIII-LIKE 3,NEI-LIKE PROTEIN 3; COMPND 6 EC: 3.2.2.-,4.2.99.18; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NEIL3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: EXPRESSION VECTOR; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSUMO KEYWDS ZINC FINGER, NEIL3-GRF, DNA REPAIR, DNA DAMAGE, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 35 AUTHOR D.C.DINESH,A.HUSKOVA,P.SRB,V.VEVERKA,J.SILHAN REVDAT 4 14-JUN-23 7OMK 1 REMARK REVDAT 3 26-OCT-22 7OMK 1 JRNL REVDAT 2 19-OCT-22 7OMK 1 JRNL REVDAT 1 01-JUN-22 7OMK 0 JRNL AUTH A.HUSKOVA,D.C.DINESH,P.SRB,E.BOURA,V.VEVERKA,J.SILHAN JRNL TITL MODEL OF ABASIC SITE DNA CROSS-LINK REPAIR; FROM THE JRNL TITL 2 ARCHITECTURE OF NEIL3 DNA BINDING DOMAINS TO THE X-STRUCTURE JRNL TITL 3 MODEL. JRNL REF NUCLEIC ACIDS RES. V. 50 10436 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 36155818 JRNL DOI 10.1093/NAR/GKAC793 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7OMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292113107. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 250 UM [U-13C; U-15N] NEIL3-GRF, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCACB; 3D HBHA(CO) REMARK 210 NH; 3D HN(CO)CA; 3D CBCA(CO)NH; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D HCCH-TOCSY; 3D H(CCO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFAM-SPARKY, YASARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 35 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 5 ARG A 514 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 514 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 29 ARG A 529 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 CYS A 515 -59.58 -123.22 REMARK 500 2 CYS A 515 -59.74 -124.15 REMARK 500 2 GLU A 595 -74.56 -129.86 REMARK 500 3 SER A 535 36.27 -141.46 REMARK 500 4 GLN A 541 172.45 179.19 REMARK 500 4 GLU A 595 55.81 26.70 REMARK 500 5 SER A 535 34.94 -142.94 REMARK 500 5 PRO A 553 -104.72 -78.03 REMARK 500 6 CYS A 515 -59.74 -124.01 REMARK 500 7 CYS A 515 -54.80 -124.07 REMARK 500 7 ASP A 523 -162.38 65.02 REMARK 500 7 GLU A 595 86.56 53.19 REMARK 500 8 CYS A 515 -56.18 -124.21 REMARK 500 8 GLU A 595 -136.57 57.94 REMARK 500 9 CYS A 515 -58.42 -123.89 REMARK 500 9 ASN A 596 21.98 -141.31 REMARK 500 10 CYS A 515 -56.65 -124.07 REMARK 500 12 CYS A 515 -55.47 -123.61 REMARK 500 13 CYS A 515 -59.71 -123.96 REMARK 500 13 ASP A 523 -178.68 63.70 REMARK 500 14 CYS A 515 -55.26 -124.04 REMARK 500 15 ASP A 523 -160.01 -179.65 REMARK 500 16 CYS A 515 -59.12 -124.15 REMARK 500 16 ASP A 523 -159.32 62.64 REMARK 500 16 ASN A 589 21.51 -72.72 REMARK 500 16 GLU A 595 -29.13 72.63 REMARK 500 17 CYS A 515 -54.66 -124.23 REMARK 500 17 ASP A 523 -160.41 176.09 REMARK 500 18 CYS A 515 -54.67 -124.05 REMARK 500 19 CYS A 515 -54.94 -123.58 REMARK 500 19 ASN A 596 -0.81 -152.05 REMARK 500 21 CYS A 515 -55.07 -123.98 REMARK 500 21 LYS A 522 -166.57 -100.07 REMARK 500 21 ASP A 523 -161.56 61.33 REMARK 500 21 GLU A 595 -34.47 44.79 REMARK 500 21 ASN A 596 -0.93 -143.41 REMARK 500 22 CYS A 515 -55.14 -124.06 REMARK 500 23 CYS A 515 -54.91 -123.88 REMARK 500 23 GLU A 595 53.59 38.24 REMARK 500 24 CYS A 515 -54.68 -124.14 REMARK 500 24 GLN A 541 -179.43 -176.41 REMARK 500 25 CYS A 515 -55.04 -123.75 REMARK 500 25 GLU A 595 0.02 59.20 REMARK 500 26 CYS A 515 -59.71 -124.16 REMARK 500 26 GLU A 595 -157.81 59.13 REMARK 500 27 GLN A 541 -179.41 -176.73 REMARK 500 27 PRO A 553 -142.81 -88.05 REMARK 500 27 GLU A 595 -161.66 57.47 REMARK 500 28 CYS A 515 -59.66 -123.98 REMARK 500 28 ASP A 523 -164.71 62.76 REMARK 500 REMARK 500 THIS ENTRY HAS 65 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34630 RELATED DB: BMRB REMARK 900 THE NMR STRUCTURE OF THE ZF-GRF DOMAINS FROM THE MOUSE ENDONUCLEASE REMARK 900 VIII-LIKE 3 (MNEIL3) DBREF 7OMK A 505 597 UNP Q8K203 NEIL3_MOUSE 505 597 SEQADV 7OMK LYS A 556 UNP Q8K203 ARG 556 VARIANT SEQADV 7OMK GLU A 585 UNP Q8K203 LYS 585 VARIANT SEQRES 1 A 93 SER PRO LEU CYS LYS MET HIS HIS ARG ARG CYS VAL LEU SEQRES 2 A 93 ARG VAL VAL ARG LYS ASP GLY GLU ASN LYS GLY ARG GLN SEQRES 3 A 93 PHE TYR ALA CYS SER LEU PRO ARG GLY ALA GLN CYS GLY SEQRES 4 A 93 PHE PHE GLU TRP ALA ASP LEU SER PHE PRO PHE CYS LYS SEQRES 5 A 93 HIS GLY LYS ARG SER ILE MET LYS THR VAL LEU LYS ILE SEQRES 6 A 93 GLY PRO ASN ASN GLY LYS ASN PHE PHE VAL CYS PRO LEU SEQRES 7 A 93 GLU LYS GLU LYS GLN CYS ASN PHE PHE GLN TRP ALA GLU SEQRES 8 A 93 ASN GLY HELIX 1 AA1 ASP A 549 PHE A 552 5 4 SHEET 1 AA1 3 VAL A 516 VAL A 519 0 SHEET 2 AA1 3 GLN A 530 ALA A 533 -1 O PHE A 531 N ARG A 518 SHEET 3 AA1 3 GLU A 546 TRP A 547 -1 O GLU A 546 N TYR A 532 SHEET 1 AA2 3 ILE A 562 THR A 565 0 SHEET 2 AA2 3 ASN A 576 VAL A 579 -1 O VAL A 579 N ILE A 562 SHEET 3 AA2 3 GLN A 592 TRP A 593 -1 O GLN A 592 N PHE A 578 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1