HEADER HYDROLASE 09-MAR-16 2NBQ TITLE NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN APOBEC3B COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DC->DU-EDITING ENZYME APOBEC-3B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 187-382; COMPND 5 SYNONYM: A3B, PHORBOLIN-1-RELATED PROTEIN, PHORBOLIN-2/3; COMPND 6 EC: 3.5.4.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: APOBEC3B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21 KEYWDS HYDROLASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR I.L.BYEON,C.BYEON,A.M.GRONENBORN REVDAT 3 14-JUN-23 2NBQ 1 REMARK SEQADV LINK REVDAT 2 29-JUN-16 2NBQ 1 JRNL REVDAT 1 01-JUN-16 2NBQ 0 JRNL AUTH I.J.BYEON,C.H.BYEON,T.WU,M.MITRA,D.SINGER,J.G.LEVIN, JRNL AUTH 2 A.M.GRONENBORN JRNL TITL NUCLEAR MAGNETIC RESONANCE STRUCTURE OF THE APOBEC3B JRNL TITL 2 CATALYTIC DOMAIN: STRUCTURAL BASIS FOR SUBSTRATE BINDING AND JRNL TITL 3 DNA DEAMINASE ACTIVITY. JRNL REF BIOCHEMISTRY V. 55 2944 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27163633 JRNL DOI 10.1021/ACS.BIOCHEM.6B00382 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH, XPLOR-NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (XPLOR REMARK 3 -NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FLEXIBLE (HEXA-HISTIDINE TAG) REMARK 3 RESIDUES WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND REMARK 3 THUS NOT SHOWN IN THE COORDINATES. REMARK 4 REMARK 4 2NBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000104668. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.08 MM [U-13C; U-15N; U-2H] REMARK 210 A3B_CTD, 0.08 MM ZINC, 10 MM DTT, REMARK 210 25 MM SODIUM PHOSPHATE, 93% H2O/ REMARK 210 7% D2O; 0.08 MM [U-100% 13C; U- REMARK 210 100% 15N] A3B_CTD, 0.08 MM ZINC, REMARK 210 10 MM DTT, 25 MM SODIUM REMARK 210 PHOSPHATE, 93% H2O/7% D2O; 0.05 REMARK 210 MM A3B_CTD, 0.05 MM ZINC, 10 MM REMARK 210 DTT, 25 MM SODIUM PHOSPHATE, 93% REMARK 210 H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D HN(COCA)CB; 3D REMARK 210 SIMULTANEOUS 13C- AND 15N-EDITED REMARK 210 NOESY; 3D TROSY-HNCACB; 3D TROSY- REMARK 210 HN(CO)CACB; 2D 1H-1H NOESY; 3D REMARK 210 HCCH-TOCSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR-NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 256 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-30 REMARK 465 RES C SSSEQI REMARK 465 LEU A 383 REMARK 465 GLU A 384 REMARK 465 HIS A 385 REMARK 465 HIS A 386 REMARK 465 HIS A 387 REMARK 465 HIS A 388 REMARK 465 HIS A 389 REMARK 465 HIS A 390 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 ARG A 190 -154.53 -125.87 REMARK 500 1 TYR A 191 -42.76 -170.96 REMARK 500 1 LEU A 192 92.54 38.29 REMARK 500 1 MET A 193 162.20 -45.51 REMARK 500 1 ASN A 204 -114.92 39.75 REMARK 500 1 LEU A 209 -60.60 -129.95 REMARK 500 1 ARG A 211 47.56 -75.64 REMARK 500 1 ARG A 212 -48.76 -138.19 REMARK 500 1 LEU A 223 97.64 -64.90 REMARK 500 1 CYS A 239 -166.50 -106.72 REMARK 500 1 ASN A 240 -77.78 -70.74 REMARK 500 1 ALA A 242 -145.50 -145.42 REMARK 500 1 GLN A 266 54.23 39.01 REMARK 500 1 LEU A 267 -179.48 -61.42 REMARK 500 1 ALA A 270 -70.13 -83.44 REMARK 500 1 GLN A 271 -178.17 -66.55 REMARK 500 1 ARG A 274 112.33 -162.34 REMARK 500 1 SER A 280 24.31 -78.92 REMARK 500 1 TRP A 281 -160.67 -164.23 REMARK 500 1 PRO A 283 161.03 -49.01 REMARK 500 1 SER A 286 -82.16 -65.65 REMARK 500 1 CYS A 289 -70.61 -98.55 REMARK 500 1 ARG A 351 87.06 -150.90 REMARK 500 1 GLN A 352 21.29 45.73 REMARK 500 1 PRO A 358 -78.00 -80.37 REMARK 500 1 TRP A 359 -80.54 -156.47 REMARK 500 1 ASP A 360 -31.79 -176.15 REMARK 500 1 LEU A 377 6.94 -65.59 REMARK 500 1 GLN A 378 -66.01 -122.68 REMARK 500 1 ASN A 379 86.91 40.28 REMARK 500 2 GLU A 187 177.81 49.86 REMARK 500 2 ASP A 205 66.87 -172.67 REMARK 500 2 PRO A 206 81.61 -48.33 REMARK 500 2 LEU A 207 -75.47 -132.86 REMARK 500 2 VAL A 208 54.77 -153.50 REMARK 500 2 ARG A 210 -38.20 -150.56 REMARK 500 2 ARG A 212 -47.99 -162.78 REMARK 500 2 LEU A 223 96.90 -69.13 REMARK 500 2 HIS A 234 26.90 -143.69 REMARK 500 2 ASN A 240 40.90 -93.48 REMARK 500 2 ALA A 242 163.54 166.12 REMARK 500 2 ASN A 244 9.11 -154.90 REMARK 500 2 LEU A 267 170.25 -52.16 REMARK 500 2 PRO A 269 -8.28 -46.84 REMARK 500 2 GLN A 271 -156.20 -134.94 REMARK 500 2 ARG A 274 118.62 -168.88 REMARK 500 2 SER A 280 44.47 -85.95 REMARK 500 2 TRP A 281 -166.26 172.13 REMARK 500 2 CYS A 284 -75.75 -74.24 REMARK 500 2 SER A 286 -76.76 -38.33 REMARK 500 REMARK 500 THIS ENTRY HAS 849 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 253 ND1 REMARK 620 2 CYS A 284 SG 109.1 REMARK 620 3 CYS A 289 SG 109.4 108.8 REMARK 620 N 1 2 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25985 RELATED DB: BMRB DBREF 2NBQ A 187 382 UNP Q9UH17 ABC3B_HUMAN 187 382 SEQADV 2NBQ MET A 186 UNP Q9UH17 EXPRESSION TAG SEQADV 2NBQ LEU A 383 UNP Q9UH17 EXPRESSION TAG SEQADV 2NBQ GLU A 384 UNP Q9UH17 EXPRESSION TAG SEQADV 2NBQ HIS A 385 UNP Q9UH17 EXPRESSION TAG SEQADV 2NBQ HIS A 386 UNP Q9UH17 EXPRESSION TAG SEQADV 2NBQ HIS A 387 UNP Q9UH17 EXPRESSION TAG SEQADV 2NBQ HIS A 388 UNP Q9UH17 EXPRESSION TAG SEQADV 2NBQ HIS A 389 UNP Q9UH17 EXPRESSION TAG SEQADV 2NBQ HIS A 390 UNP Q9UH17 EXPRESSION TAG SEQRES 1 A 205 MET GLU ILE LEU ARG TYR LEU MET ASP PRO ASP THR PHE SEQRES 2 A 205 THR PHE ASN PHE ASN ASN ASP PRO LEU VAL LEU ARG ARG SEQRES 3 A 205 ARG GLN THR TYR LEU CYS TYR GLU VAL GLU ARG LEU ASP SEQRES 4 A 205 ASN GLY THR TRP VAL LEU MET ASP GLN HIS MET GLY PHE SEQRES 5 A 205 LEU CYS ASN GLU ALA LYS ASN LEU LEU CYS GLY PHE TYR SEQRES 6 A 205 GLY ARG HIS ALA GLU LEU ARG PHE LEU ASP LEU VAL PRO SEQRES 7 A 205 SER LEU GLN LEU ASP PRO ALA GLN ILE TYR ARG VAL THR SEQRES 8 A 205 TRP PHE ILE SER TRP SER PRO CYS PHE SER TRP GLY CYS SEQRES 9 A 205 ALA GLY GLU VAL ARG ALA PHE LEU GLN GLU ASN THR HIS SEQRES 10 A 205 VAL ARG LEU ARG ILE PHE ALA ALA ARG ILE TYR ASP TYR SEQRES 11 A 205 ASP PRO LEU TYR LYS GLU ALA LEU GLN MET LEU ARG ASP SEQRES 12 A 205 ALA GLY ALA GLN VAL SER ILE MET THR TYR ASP GLU PHE SEQRES 13 A 205 GLU TYR CYS TRP ASP THR PHE VAL TYR ARG GLN GLY CYS SEQRES 14 A 205 PRO PHE GLN PRO TRP ASP GLY LEU GLU GLU HIS SER GLN SEQRES 15 A 205 ALA LEU SER GLY ARG LEU ARG ALA ILE LEU GLN ASN GLN SEQRES 16 A 205 GLY ASN LEU GLU HIS HIS HIS HIS HIS HIS HET ZN A 500 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 PRO A 195 PHE A 202 1 8 HELIX 2 2 ALA A 254 LEU A 265 1 12 HELIX 3 3 CYS A 289 GLU A 299 1 11 HELIX 4 7 TYR A 319 ALA A 329 1 11 HELIX 5 8 TYR A 338 PHE A 348 1 11 HELIX 6 9 GLY A 361 LEU A 377 1 17 SHEET 1 A 3 THR A 227 LEU A 230 0 SHEET 2 A 3 TYR A 215 ASP A 224 -1 N ASP A 224 O THR A 227 SHEET 3 A 3 GLY A 236 CYS A 239 -1 O LEU A 238 N LEU A 216 SHEET 1 B 5 THR A 227 LEU A 230 0 SHEET 2 B 5 TYR A 215 ASP A 224 -1 N ASP A 224 O THR A 227 SHEET 3 B 5 TYR A 273 ILE A 279 -1 O PHE A 278 N CYS A 217 SHEET 4 B 5 VAL A 303 ALA A 309 1 O ARG A 306 N TRP A 277 SHEET 5 B 5 GLN A 332 ILE A 335 1 O GLN A 332 N ILE A 307 LINK ND1 HIS A 253 ZN ZN A 500 1555 1555 2.30 LINK SG CYS A 284 ZN ZN A 500 1555 1555 2.30 LINK SG CYS A 289 ZN ZN A 500 1555 1555 2.30 SITE 1 AC1 3 HIS A 253 CYS A 284 CYS A 289 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