HEADER DNA BINDING PROTEIN/DNA 21-JAN-25 9LNP TITLE THE HUNG BOUND TO DNA PRODUCT EMBEDDING URIDINE RIBONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*T*(RP5)P*AP*TP*CP*TP*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SYTHESIZED DNA OLIGO EMBEDING RU; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 12 CHAIN: E; COMPND 13 SYNONYM: UDG; COMPND 14 EC: 3.2.2.27; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UNG, DGU, UNG1, UNG15; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS URACIL DNA GLYCOSYLASE URIDINE RIBONUCLEOTIDE DNA DAMAGE BASE KEYWDS 2 EXCISION REPAIR, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,C.ZHOU,X.ZHAN,C.FAN REVDAT 1 16-APR-25 9LNP 0 JRNL AUTH C.FAN,X.ZHAN,F.GUO,Q.LI,K.LU,X.SHAN,Y.ZHOU,M.REN, JRNL AUTH 2 M.M.GREENBERG,Y.LIU,C.ZHOU JRNL TITL URIDINE EMBEDDED WITHIN DNA IS REPAIRED BY URACIL DNA JRNL TITL 2 GLYCOSYLASE VIA A MECHANISM DISTINCT FROM THAT OF JRNL TITL 3 RIBONUCLEASE H2. JRNL REF J.AM.CHEM.SOC. V. 147 11574 2025 JRNL REFN ESSN 1520-5126 JRNL PMID 40130361 JRNL DOI 10.1021/JACS.5C01436 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 60661 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 2939 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.7900 - 4.8300 0.99 2748 144 0.1487 0.1640 REMARK 3 2 4.8300 - 3.8500 1.00 2777 126 0.1188 0.1348 REMARK 3 3 3.8500 - 3.3600 1.00 2742 159 0.1345 0.1773 REMARK 3 4 3.3600 - 3.0600 1.00 2760 151 0.1468 0.1785 REMARK 3 5 3.0600 - 2.8400 1.00 2742 160 0.1650 0.2646 REMARK 3 6 2.8400 - 2.6700 1.00 2810 127 0.1750 0.2189 REMARK 3 7 2.6700 - 2.5400 1.00 2749 132 0.1620 0.1979 REMARK 3 8 2.5400 - 2.4300 1.00 2734 150 0.1686 0.2116 REMARK 3 9 2.4300 - 2.3300 1.00 2767 121 0.1630 0.2223 REMARK 3 10 2.3300 - 2.2500 1.00 2775 150 0.1693 0.2044 REMARK 3 11 2.2500 - 2.1800 1.00 2791 119 0.1731 0.2107 REMARK 3 12 2.1800 - 2.1200 1.00 2773 134 0.1877 0.2441 REMARK 3 13 2.1200 - 2.0600 1.00 2792 130 0.1925 0.2402 REMARK 3 14 2.0600 - 2.0100 0.99 2715 140 0.2042 0.2475 REMARK 3 15 2.0100 - 1.9700 1.00 2775 135 0.2232 0.2378 REMARK 3 16 1.9700 - 1.9300 0.99 2712 146 0.2477 0.3005 REMARK 3 17 1.9300 - 1.8900 1.00 2755 126 0.2712 0.3326 REMARK 3 18 1.8900 - 1.8500 0.99 2745 144 0.2729 0.2971 REMARK 3 19 1.8500 - 1.8200 1.00 2718 165 0.2806 0.3077 REMARK 3 20 1.8200 - 1.7900 0.98 2742 148 0.3166 0.3592 REMARK 3 21 1.7900 - 1.7600 0.94 2600 132 0.3385 0.3894 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9LNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 31-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300056035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 414484 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 19.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.18600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% POLYETHYLENE GLYCOL 4000 REMARK 280 (SIGMA)/100 MM HEPES BUFFER (PH 6.5)/10% DIOXANE/1 MM DTT, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.76500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.64500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.76500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.64500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH E 701 O HOH E 716 2.05 REMARK 500 OE2 GLU E 219 O HOH E 501 2.08 REMARK 500 O HOH E 674 O HOH E 703 2.15 REMARK 500 O HOH B 118 O HOH B 126 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT A 9 O3' DT A 9 C3' -0.059 REMARK 500 DA B 2 O3' DA B 2 C3' -0.063 REMARK 500 REMARK 500 REMARK: NULL 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 DA B 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA B 10 O4' - C1' - N9 ANGL. DEV. = 1.8 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 GLN E 152 -75.00 -98.06 REMARK 500 HIS E 154 23.07 -140.29 REMARK 500 PHE E 158 -3.86 77.90 REMARK 500 HIS E 212 -0.59 70.28 REMARK 500 ARG E 260 -31.51 -130.91 REMARK 500 SER E 273 -6.24 -140.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 127 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH E 761 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH E 762 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH E 763 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH E 764 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH E 765 DISTANCE = 8.01 ANGSTROMS REMARK 525 HOH E 766 DISTANCE = 8.07 ANGSTROMS REMARK 525 HOH E 767 DISTANCE = 8.70 ANGSTROMS DBREF 9LNP A 2 10 PDB 9LNP 9LNP 2 10 DBREF 9LNP B 1 10 PDB 9LNP 9LNP 1 10 DBREF 9LNP E 85 304 UNP P13051 UNG_HUMAN 94 313 SEQADV 9LNP GLY E 81 UNP P13051 EXPRESSION TAG SEQADV 9LNP SER E 82 UNP P13051 EXPRESSION TAG SEQADV 9LNP HIS E 83 UNP P13051 EXPRESSION TAG SEQADV 9LNP MET E 84 UNP P13051 EXPRESSION TAG SEQRES 1 A 9 DT DG DT RP5 DA DT DC DT DT SEQRES 1 B 10 DA DA DA DG DA DT DA DA DC DA SEQRES 1 E 224 GLY SER HIS MET PHE GLY GLU SER TRP LYS LYS HIS LEU SEQRES 2 E 224 SER GLY GLU PHE GLY LYS PRO TYR PHE ILE LYS LEU MET SEQRES 3 E 224 GLY PHE VAL ALA GLU GLU ARG LYS HIS TYR THR VAL TYR SEQRES 4 E 224 PRO PRO PRO HIS GLN VAL PHE THR TRP THR GLN MET CYS SEQRES 5 E 224 ASP ILE LYS ASP VAL LYS VAL VAL ILE LEU GLY GLN ASP SEQRES 6 E 224 PRO TYR HIS GLY PRO ASN GLN ALA HIS GLY LEU CYS PHE SEQRES 7 E 224 SER VAL GLN ARG PRO VAL PRO PRO PRO PRO SER LEU GLU SEQRES 8 E 224 ASN ILE TYR LYS GLU LEU SER THR ASP ILE GLU ASP PHE SEQRES 9 E 224 VAL HIS PRO GLY HIS GLY ASP LEU SER GLY TRP ALA LYS SEQRES 10 E 224 GLN GLY VAL LEU LEU LEU ASN ALA VAL LEU THR VAL ARG SEQRES 11 E 224 ALA HIS GLN ALA ASN SER HIS LYS GLU ARG GLY TRP GLU SEQRES 12 E 224 GLN PHE THR ASP ALA VAL VAL SER TRP LEU ASN GLN ASN SEQRES 13 E 224 SER ASN GLY LEU VAL PHE LEU LEU TRP GLY SER TYR ALA SEQRES 14 E 224 GLN LYS LYS GLY SER ALA ILE ASP ARG LYS ARG HIS HIS SEQRES 15 E 224 VAL LEU GLN THR ALA HIS PRO SER PRO LEU SER VAL TYR SEQRES 16 E 224 ARG GLY PHE PHE GLY CYS ARG HIS PHE SER LYS THR ASN SEQRES 17 E 224 GLU LEU LEU GLN LYS SER GLY LYS LYS PRO ILE ASP TRP SEQRES 18 E 224 LYS GLU LEU HET RP5 A 5 13 HET CA E 401 1 HETNAM RP5 5-O-PHOSPHONO-BETA-D-RIBOFURANOSE HETNAM CA CALCIUM ION HETSYN RP5 [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2- HETSYN 2 RP5 YL]METHYL DIHYDROGEN PHOSPHATE; 5-O-PHOSPHONO-BETA-D- HETSYN 3 RP5 RIBOSE; 5-O-PHOSPHONO-D-RIBOSE; 5-O-PHOSPHONO-RIBOSE FORMUL 1 RP5 C5 H11 O8 P FORMUL 4 CA CA 2+ FORMUL 5 HOH *325(H2 O) HELIX 1 AA1 GLY E 86 SER E 94 1 9 HELIX 2 AA2 GLY E 95 GLY E 98 5 4 HELIX 3 AA3 LYS E 99 TYR E 116 1 18 HELIX 4 AA4 PRO E 121 VAL E 125 5 5 HELIX 5 AA5 PHE E 126 GLN E 130 5 5 HELIX 6 AA6 ASP E 133 VAL E 137 5 5 HELIX 7 AA7 PRO E 167 ILE E 181 1 15 HELIX 8 AA8 LEU E 192 GLN E 198 1 7 HELIX 9 AA9 GLY E 221 SER E 237 1 17 HELIX 10 AB1 GLY E 246 LYS E 251 1 6 HELIX 11 AB2 LYS E 252 ILE E 256 5 5 HELIX 12 AB3 ARG E 282 SER E 294 1 13 SHEET 1 AA1 2 VAL E 118 TYR E 119 0 SHEET 2 AA1 2 VAL E 209 ARG E 210 -1 O VAL E 209 N TYR E 119 SHEET 1 AA2 4 VAL E 200 ASN E 204 0 SHEET 2 AA2 4 VAL E 139 GLY E 143 1 N VAL E 139 O LEU E 201 SHEET 3 AA2 4 VAL E 241 TRP E 245 1 O LEU E 243 N VAL E 140 SHEET 4 AA2 4 HIS E 262 THR E 266 1 O HIS E 262 N PHE E 242 LINK O3' DT A 4 P' RP5 A 5 1555 1555 1.56 LINK O3 RP5 A 5 P DA A 6 1555 1555 1.55 LINK O HOH A 114 CA CA E 401 1555 1555 2.89 CISPEP 1 TYR E 119 PRO E 120 0 -6.71 CISPEP 2 ARG E 162 PRO E 163 0 4.36 CRYST1 48.930 65.290 99.530 90.00 90.00 90.00 P 21 21 21 4 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 0.020437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015316 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010047 0.00000 CONECT 48 69 CONECT 60 61 62 72 CONECT 61 60 66 CONECT 62 60 63 64 CONECT 63 62 CONECT 64 62 65 66 CONECT 65 64 73 CONECT 66 61 64 67 CONECT 67 66 68 CONECT 68 67 69 CONECT 69 48 68 70 71 CONECT 70 69 CONECT 71 69 CONECT 72 60 CONECT 73 65 CONECT 3893 3907 CONECT 3907 3893 MASTER 310 0 2 12 6 0 0 6 2510 3 17 20 END