HEADER HYDROLASE 21-MAR-13 2M65 TITLE NMR STRUCTURE OF HUMAN RESTRICTION FACTOR APOBEC3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE DNA DC->DU-EDITING ENZYME APOBEC-3A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHORBOLIN-1; COMPND 5 EC: 3.5.4.-; COMPND 6 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: APOBEC3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS APOBEC3A, CYTIDINE DEAMINASE, ANTIVIRAL DEFENSE, HOST-VIRUS KEYWDS 2 INTERACTION, ZINC-BINDING, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR I.L.BYEON,C.BYEON,J.AHN,A.M.GRONENBORN REVDAT 5 15-MAY-24 2M65 1 REMARK REVDAT 4 14-JUN-23 2M65 1 REMARK SEQADV REVDAT 3 19-JUN-13 2M65 1 JRNL REVDAT 2 05-JUN-13 2M65 1 JRNL REVDAT 1 22-MAY-13 2M65 0 JRNL AUTH I.J.BYEON,J.AHN,M.MITRA,C.H.BYEON,K.HERCIK,J.HRITZ, JRNL AUTH 2 L.M.CHARLTON,J.G.LEVIN,A.M.GRONENBORN JRNL TITL NMR STRUCTURE OF HUMAN RESTRICTION FACTOR APOBEC3A REVEALS JRNL TITL 2 SUBSTRATE BINDING AND ENZYME SPECIFICITY. JRNL REF NAT COMMUN V. 4 1890 2013 JRNL REFN ESSN 2041-1723 JRNL PMID 23695684 JRNL DOI 10.1038/NCOMMS2883 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, C.D. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M65 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000103257. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 13C,15N-APOBEC3A, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D HN(COCA) REMARK 210 CB; 3D HCCH-TOCSY; 3D REMARK 210 SIMULANEOUS 1H-13C AND 1H-15N REMARK 210 NOESY; 3D SIMULTANEOUS 1H-13C REMARK 210 AND 1H-15N NOESY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-1H NOESY; 2D 1H- REMARK 210 1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 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 : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 512 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 200 REMARK 465 GLU A 201 REMARK 465 HIS A 202 REMARK 465 HIS A 203 REMARK 465 HIS A 204 REMARK 465 HIS A 205 REMARK 465 HIS A 206 REMARK 465 HIS A 207 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 GLU A 2 102.88 -161.18 REMARK 500 1 ALA A 3 -99.55 43.03 REMARK 500 1 SER A 7 -115.74 -104.98 REMARK 500 1 PRO A 9 28.96 -76.61 REMARK 500 1 ARG A 10 -136.31 -77.06 REMARK 500 1 HIS A 11 73.79 -107.42 REMARK 500 1 ASN A 23 95.89 -50.09 REMARK 500 1 ILE A 26 -165.92 -108.12 REMARK 500 1 ARG A 28 120.16 -172.02 REMARK 500 1 HIS A 29 -86.05 -164.70 REMARK 500 1 LYS A 30 110.91 -172.94 REMARK 500 1 GLN A 50 71.65 -102.20 REMARK 500 1 HIS A 51 -12.20 -166.76 REMARK 500 1 ASN A 57 162.95 -40.81 REMARK 500 1 ALA A 59 68.22 -160.29 REMARK 500 1 LYS A 60 14.71 -147.49 REMARK 500 1 ASN A 61 23.62 -143.24 REMARK 500 1 TYR A 67 162.45 -46.33 REMARK 500 1 LEU A 76 -19.89 -49.82 REMARK 500 1 LEU A 84 155.98 -38.75 REMARK 500 1 PRO A 86 -7.38 -49.10 REMARK 500 1 CYS A 101 -131.73 -107.77 REMARK 500 1 PHE A 102 99.69 -56.22 REMARK 500 1 SER A 103 -25.17 -38.55 REMARK 500 1 THR A 118 4.60 -66.31 REMARK 500 1 TYR A 130 119.68 -172.62 REMARK 500 1 PRO A 134 3.80 -69.72 REMARK 500 1 TRP A 162 -70.13 -64.17 REMARK 500 1 ASP A 167 35.20 -80.84 REMARK 500 1 HIS A 168 -13.46 -45.49 REMARK 500 1 GLN A 169 12.96 48.06 REMARK 500 2 GLU A 2 65.22 -69.04 REMARK 500 2 ALA A 6 -141.32 -172.40 REMARK 500 2 SER A 7 -127.70 55.05 REMARK 500 2 PRO A 9 22.69 -72.05 REMARK 500 2 ARG A 10 154.62 60.48 REMARK 500 2 HIS A 11 99.00 -161.55 REMARK 500 2 LYS A 30 62.15 -172.81 REMARK 500 2 HIS A 51 9.89 -171.51 REMARK 500 2 ASN A 57 -162.13 -70.34 REMARK 500 2 GLN A 58 172.92 51.76 REMARK 500 2 ALA A 59 -22.29 -164.88 REMARK 500 2 LYS A 60 96.68 60.67 REMARK 500 2 LEU A 62 -15.94 -43.31 REMARK 500 2 PHE A 66 65.49 -158.77 REMARK 500 2 ALA A 87 -94.87 -42.11 REMARK 500 2 PRO A 100 172.10 -42.34 REMARK 500 2 PHE A 102 109.21 -171.48 REMARK 500 2 ASN A 117 61.88 -164.29 REMARK 500 2 THR A 118 2.84 -59.29 REMARK 500 REMARK 500 THIS ENTRY HAS 788 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 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 70 ND1 REMARK 620 2 CYS A 101 SG 108.9 REMARK 620 3 CYS A 106 SG 109.1 109.4 REMARK 620 N 1 2 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 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19108 RELATED DB: BMRB DBREF 2M65 A 1 199 UNP P31941 ABC3A_HUMAN 1 199 SEQADV 2M65 LEU A 200 UNP P31941 EXPRESSION TAG SEQADV 2M65 GLU A 201 UNP P31941 EXPRESSION TAG SEQADV 2M65 HIS A 202 UNP P31941 EXPRESSION TAG SEQADV 2M65 HIS A 203 UNP P31941 EXPRESSION TAG SEQADV 2M65 HIS A 204 UNP P31941 EXPRESSION TAG SEQADV 2M65 HIS A 205 UNP P31941 EXPRESSION TAG SEQADV 2M65 HIS A 206 UNP P31941 EXPRESSION TAG SEQADV 2M65 HIS A 207 UNP P31941 EXPRESSION TAG SEQRES 1 A 207 MET GLU ALA SER PRO ALA SER GLY PRO ARG HIS LEU MET SEQRES 2 A 207 ASP PRO HIS ILE PHE THR SER ASN PHE ASN ASN GLY ILE SEQRES 3 A 207 GLY ARG HIS LYS THR TYR LEU CYS TYR GLU VAL GLU ARG SEQRES 4 A 207 LEU ASP ASN GLY THR SER VAL LYS MET ASP GLN HIS ARG SEQRES 5 A 207 GLY PHE LEU HIS ASN GLN ALA LYS ASN LEU LEU CYS GLY SEQRES 6 A 207 PHE TYR GLY ARG HIS ALA GLU LEU ARG PHE LEU ASP LEU SEQRES 7 A 207 VAL PRO SER LEU GLN LEU ASP PRO ALA GLN ILE TYR ARG SEQRES 8 A 207 VAL THR TRP PHE ILE SER TRP SER PRO CYS PHE SER TRP SEQRES 9 A 207 GLY CYS ALA GLY GLU VAL ARG ALA PHE LEU GLN GLU ASN SEQRES 10 A 207 THR HIS VAL ARG LEU ARG ILE PHE ALA ALA ARG ILE TYR SEQRES 11 A 207 ASP TYR ASP PRO LEU TYR LYS GLU ALA LEU GLN MET LEU SEQRES 12 A 207 ARG ASP ALA GLY ALA GLN VAL SER ILE MET THR TYR ASP SEQRES 13 A 207 GLU PHE LYS HIS CYS TRP ASP THR PHE VAL ASP HIS GLN SEQRES 14 A 207 GLY CYS PRO PHE GLN PRO TRP ASP GLY LEU ASP GLU HIS SEQRES 15 A 207 SER GLN ALA LEU SER GLY ARG LEU ARG ALA ILE LEU GLN SEQRES 16 A 207 ASN GLN GLY ASN LEU GLU HIS HIS HIS HIS HIS HIS HET ZN A 300 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 14 PHE A 22 1 9 HELIX 2 2 HIS A 70 ASP A 77 1 8 HELIX 3 3 LEU A 78 GLN A 83 1 6 HELIX 4 4 GLY A 105 THR A 118 1 14 HELIX 5 5 LEU A 135 ASP A 145 1 11 HELIX 6 6 THR A 154 VAL A 166 1 13 HELIX 7 7 GLY A 178 GLN A 195 1 18 SHEET 1 A 3 THR A 44 LYS A 47 0 SHEET 2 A 3 TYR A 32 ASP A 41 -1 N ARG A 39 O VAL A 46 SHEET 3 A 3 GLY A 53 HIS A 56 -1 O LEU A 55 N LEU A 33 SHEET 1 B 5 THR A 44 LYS A 47 0 SHEET 2 B 5 TYR A 32 ASP A 41 -1 N ARG A 39 O VAL A 46 SHEET 3 B 5 ILE A 89 TRP A 98 -1 O ARG A 91 N GLU A 38 SHEET 4 B 5 VAL A 120 ARG A 128 1 O ALA A 127 N ILE A 96 SHEET 5 B 5 GLN A 149 ILE A 152 1 O GLN A 149 N ILE A 124 LINK ND1 HIS A 70 ZN ZN A 300 1555 1555 2.30 LINK SG CYS A 101 ZN ZN A 300 1555 1555 2.30 LINK SG CYS A 106 ZN ZN A 300 1555 1555 2.30 SITE 1 AC1 3 HIS A 70 CYS A 101 CYS A 106 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