HEADER RNA BINDING PROTEIN 23-FEB-15 2MZQ TITLE NMR STRUCTURE OF THE RRM3 DOMAIN OF GBP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-STRAND TELOMERIC DNA-BINDING PROTEIN GBP2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THIRD RRM DOMAIN (UNP RESIDUES 329-427); COMPND 5 SYNONYM: G-STRAND-BINDING PROTEIN 2, RAP1 LOCALIZATION FACTOR 6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: GBP2, RLF6, YCL011C, YCL11C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS RRM, RNA BINDING DOMAIN, GBP2, THO/TREX, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.MARTINEZ-LUMBRERAS,B.SERAPHIN,J.PEREZ-CANADILLAS REVDAT 5 15-MAY-24 2MZQ 1 REMARK REVDAT 4 14-JUN-23 2MZQ 1 REMARK SEQADV REVDAT 3 27-JAN-16 2MZQ 1 JRNL REVDAT 2 09-DEC-15 2MZQ 1 JRNL REVDAT 1 02-DEC-15 2MZQ 0 JRNL AUTH S.MARTINEZ-LUMBRERAS,V.TAVERNITI,S.ZORRILLA,B.SERAPHIN, JRNL AUTH 2 J.M.PEREZ-CANADILLAS JRNL TITL GBP2 INTERACTS WITH THO/TREX THROUGH A NOVEL TYPE OF RRM JRNL TITL 2 DOMAIN. JRNL REF NUCLEIC ACIDS RES. V. 44 437 2016 JRNL REFN ISSN 0305-1048 JRNL PMID 26602689 JRNL DOI 10.1093/NAR/GKV1303 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MZQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000104239. 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 : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM PROTEIN, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 0.1 MM DTT, 90% H2O/10% D2O; REMARK 210 0.8 MM PROTEIN, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 0.1 MM DTT, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 3D HNCA; 3D HNCO; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, TOPSPIN, CCPNMR ANALYSIS, REMARK 210 NMRPIPE REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 1 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 5 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 7 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 8 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 TYR A 423 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 12 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 14 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 14 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 15 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 17 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 18 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 18 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 19 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 19 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 20 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 20 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -3.6 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 ILE A 330 -46.00 -160.34 REMARK 500 1 ASP A 331 4.70 -151.54 REMARK 500 1 ASN A 348 -78.15 -74.77 REMARK 500 1 CYS A 349 -32.60 161.65 REMARK 500 1 ASN A 410 28.88 -75.45 REMARK 500 1 ASN A 411 9.33 -160.41 REMARK 500 2 ILE A 330 -47.31 -165.19 REMARK 500 2 ASN A 348 -78.95 -77.21 REMARK 500 2 CYS A 349 -28.65 162.56 REMARK 500 2 ASN A 410 34.47 -77.48 REMARK 500 2 ASN A 411 12.76 -174.49 REMARK 500 3 SER A 328 -48.18 -174.54 REMARK 500 3 ASP A 331 -33.67 68.92 REMARK 500 3 ASP A 346 44.20 -148.90 REMARK 500 3 ARG A 347 61.91 63.34 REMARK 500 3 ASN A 348 -62.48 -103.51 REMARK 500 3 CYS A 349 -25.44 166.06 REMARK 500 3 LYS A 374 78.92 -110.86 REMARK 500 3 ASN A 410 13.33 -64.82 REMARK 500 3 ASN A 411 12.53 -157.66 REMARK 500 4 ILE A 330 -11.48 -144.40 REMARK 500 4 CYS A 349 -44.85 158.51 REMARK 500 4 ALA A 378 138.05 -170.46 REMARK 500 5 ILE A 330 -47.21 -160.77 REMARK 500 5 ASP A 331 -1.53 -152.55 REMARK 500 5 ASN A 348 -74.63 -81.30 REMARK 500 5 CYS A 349 -22.39 156.89 REMARK 500 6 ASP A 346 72.60 -103.51 REMARK 500 6 ARG A 347 63.91 60.79 REMARK 500 6 ASN A 348 -153.51 -89.65 REMARK 500 6 ASN A 411 -14.01 166.18 REMARK 500 7 SER A 328 -47.70 -165.40 REMARK 500 7 ASN A 348 -77.38 -74.70 REMARK 500 7 CYS A 349 -27.07 160.42 REMARK 500 7 ASN A 411 -14.41 166.50 REMARK 500 8 ASP A 331 -48.00 -26.28 REMARK 500 8 ARG A 347 67.83 73.29 REMARK 500 8 ASN A 348 -149.40 -99.94 REMARK 500 8 ASN A 410 35.57 -77.48 REMARK 500 8 ASN A 411 9.70 -171.00 REMARK 500 9 SER A 328 -162.66 -160.75 REMARK 500 9 ASN A 348 -142.63 -92.00 REMARK 500 9 LYS A 374 78.48 -101.81 REMARK 500 11 ILE A 330 25.41 -146.94 REMARK 500 11 ARG A 347 61.21 61.90 REMARK 500 11 ASN A 348 -157.06 -88.70 REMARK 500 11 ALA A 378 138.50 -171.85 REMARK 500 11 ASN A 410 35.64 -76.97 REMARK 500 11 ASN A 411 12.38 -173.52 REMARK 500 12 ASP A 346 65.03 -100.04 REMARK 500 REMARK 500 THIS ENTRY HAS 103 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 345 ASP A 346 14 -149.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 414 0.08 SIDE CHAIN REMARK 500 2 TYR A 414 0.08 SIDE CHAIN REMARK 500 3 TYR A 414 0.09 SIDE CHAIN REMARK 500 4 TYR A 414 0.09 SIDE CHAIN REMARK 500 11 ARG A 362 0.08 SIDE CHAIN REMARK 500 12 TYR A 414 0.08 SIDE CHAIN REMARK 500 13 TYR A 414 0.08 SIDE CHAIN REMARK 500 14 TYR A 414 0.09 SIDE CHAIN REMARK 500 18 ARG A 347 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25496 RELATED DB: BMRB REMARK 900 RELATED ID: 2MZR RELATED DB: PDB REMARK 900 RELATED ID: 2MZS RELATED DB: PDB REMARK 900 RELATED ID: 2MZT RELATED DB: PDB DBREF 2MZQ A 329 427 UNP P25555 GBP2_YEAST 329 427 SEQADV 2MZQ GLY A 327 UNP P25555 EXPRESSION TAG SEQADV 2MZQ SER A 328 UNP P25555 EXPRESSION TAG SEQRES 1 A 101 GLY SER HIS ILE ASP GLU THR ALA ALA LYS PHE THR GLU SEQRES 2 A 101 GLY VAL ASN PRO GLY GLY ASP ARG ASN CYS PHE ILE TYR SEQRES 3 A 101 CYS SER ASN LEU PRO PHE SER THR ALA ARG SER ASP LEU SEQRES 4 A 101 PHE ASP LEU PHE GLY PRO ILE GLY LYS ILE ASN ASN ALA SEQRES 5 A 101 GLU LEU LYS PRO GLN GLU ASN GLY GLN PRO THR GLY VAL SEQRES 6 A 101 ALA VAL VAL GLU TYR GLU ASN LEU VAL ASP ALA ASP PHE SEQRES 7 A 101 CYS ILE GLN LYS LEU ASN ASN TYR ASN TYR GLY GLY CYS SEQRES 8 A 101 SER LEU GLN ILE SER TYR ALA ARG ARG ASP HELIX 1 1 ASP A 331 PHE A 337 1 7 HELIX 2 2 ALA A 361 SER A 363 5 3 HELIX 3 3 ASP A 364 PHE A 369 1 6 HELIX 4 4 ASN A 398 LEU A 409 1 12 SHEET 1 A 4 ILE A 375 LEU A 380 0 SHEET 2 A 4 VAL A 391 TYR A 396 -1 O VAL A 393 N GLU A 379 SHEET 3 A 4 PHE A 350 SER A 354 -1 N ILE A 351 O VAL A 394 SHEET 4 A 4 GLN A 420 TYR A 423 -1 O GLN A 420 N SER A 354 SHEET 1 B 2 ASN A 413 TYR A 414 0 SHEET 2 B 2 CYS A 417 SER A 418 -1 O CYS A 417 N TYR A 414 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