HEADER HYDROLASE 13-MAY-25 9OMC TITLE CRYSTAL STRUCTURE OF E. COLI APAH IN COMPLEX WITH GP4G COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIS(5'-NUCLEOSYL)-TETRAPHOSPHATASE [SYMMETRICAL]; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AP4A HYDROLASE,DIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE COMPND 5 PYROPHOSPHOHYDROLASE,DIADENOSINE TETRAPHOSPHATASE; COMPND 6 EC: 3.6.1.41; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: APAH, B0049, JW0048; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS APAH, SYMMETRICAL HYDROLASE, RNA DECAPPING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.NUTHANAKANTI,A.SERGANOV REVDAT 1 03-SEP-25 9OMC 0 JRNL AUTH A.NUTHANAKANTI,M.KORN,R.LEVENSON-PALMER,Y.WU,N.R.BABU, JRNL AUTH 2 X.HUANG,R.S.BANH,J.G.BELASCO,A.SERGANOV JRNL TITL APAH DECAPS NP 4 N-CAPPED RNAS IN TWO ALTERNATIVE JRNL TITL 2 ORIENTATIONS. JRNL REF NAT.CHEM.BIOL. 2025 JRNL REFN ESSN 1552-4469 JRNL PMID 40789943 JRNL DOI 10.1038/S41589-025-01991-4 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 50813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2009 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 28.2200 - 4.9300 0.98 3669 156 0.1721 0.1749 REMARK 3 2 4.9300 - 3.9100 0.98 3562 143 0.1438 0.1721 REMARK 3 3 3.9100 - 3.4200 0.98 3522 147 0.1541 0.1531 REMARK 3 4 3.4200 - 3.1100 0.98 3553 146 0.1796 0.2073 REMARK 3 5 3.1100 - 2.8800 0.98 3536 141 0.1873 0.2417 REMARK 3 6 2.8800 - 2.7100 0.98 3502 155 0.1909 0.2174 REMARK 3 7 2.7100 - 2.5800 0.98 3507 123 0.1975 0.2615 REMARK 3 8 2.5800 - 2.4700 0.98 3482 163 0.1872 0.2224 REMARK 3 9 2.4700 - 2.3700 0.98 3508 131 0.2004 0.2325 REMARK 3 10 2.3700 - 2.2900 0.98 3467 150 0.2143 0.2315 REMARK 3 11 2.2900 - 2.2200 0.98 3508 141 0.2150 0.2483 REMARK 3 12 2.2200 - 2.1500 0.98 3462 144 0.2188 0.2451 REMARK 3 13 2.1500 - 2.1000 0.97 3465 128 0.2437 0.2207 REMARK 3 14 2.1000 - 2.0500 0.86 3061 141 0.3483 0.4166 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 4412 REMARK 3 ANGLE : 0.970 6035 REMARK 3 CHIRALITY : 0.053 644 REMARK 3 PLANARITY : 0.007 768 REMARK 3 DIHEDRAL : 10.930 602 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 9OMC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000295865. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : FAST_DP REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51087 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 28.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.90500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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 (%): 64.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CONDITIONS: 0.3 MM APAH (10 MG/ML), 1 REMARK 280 MM DTT, 3 MM MGCL2, 10 MM CA(OAC)2, 25 MM HEPES (PH 7.5), 0.2 M REMARK 280 NACL AND SOAKED WITH GP4G. WELL SOLUTION: 0.24 M SODIUM MALONATE REMARK 280 (PH 7.0), 20% PEG3350., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 82.87750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.28100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 82.87750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.28100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 HIS A 271 REMARK 465 LYS A 272 REMARK 465 ASP A 273 REMARK 465 LEU A 274 REMARK 465 GLY A 275 REMARK 465 GLU A 276 REMARK 465 ALA A 277 REMARK 465 ALA A 278 REMARK 465 ALA A 279 REMARK 465 SER A 280 REMARK 465 HIS A 281 REMARK 465 HIS A 282 REMARK 465 HIS A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 REMARK 465 HIS A 286 REMARK 465 MET B 1 REMARK 465 HIS B 271 REMARK 465 LYS B 272 REMARK 465 ASP B 273 REMARK 465 LEU B 274 REMARK 465 GLY B 275 REMARK 465 GLU B 276 REMARK 465 ALA B 277 REMARK 465 ALA B 278 REMARK 465 ALA B 279 REMARK 465 SER B 280 REMARK 465 HIS B 281 REMARK 465 HIS B 282 REMARK 465 HIS B 283 REMARK 465 HIS B 284 REMARK 465 HIS B 285 REMARK 465 HIS B 286 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 ARG A 79 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 83 CD CE NZ REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 201 CD OE1 OE2 REMARK 470 LYS A 208 CE NZ REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 ARG A 270 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 LYS B 81 CE NZ REMARK 470 LYS B 83 CD CE NZ REMARK 470 GLU B 201 CD OE1 OE2 REMARK 470 GLU B 202 CD OE1 OE2 REMARK 470 LYS B 208 CE NZ REMARK 470 GLU B 238 CG CD OE1 OE2 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 O2B BKP A 301 O HOH A 401 1.92 REMARK 500 O HOH A 533 O HOH A 560 2.12 REMARK 500 NZ LYS B 197 O4G BKP B 402 2.16 REMARK 500 O HOH A 562 O HOH A 581 2.18 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 ALA A 40 149.45 78.84 REMARK 500 ARG A 41 -61.28 74.84 REMARK 500 ARG A 184 -73.70 -135.99 REMARK 500 PRO A 206 32.40 -95.06 REMARK 500 HIS A 227 -56.99 68.70 REMARK 500 ALA B 40 151.22 77.69 REMARK 500 ARG B 41 -61.18 73.94 REMARK 500 ARG B 184 -73.35 -135.87 REMARK 500 PRO B 206 30.68 -97.52 REMARK 500 HIS B 227 -54.26 68.33 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 MN A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD2 REMARK 620 2 HIS A 10 NE2 118.6 REMARK 620 3 ASP A 37 OD2 88.2 97.0 REMARK 620 4 BKP A 301 O1B 161.3 78.0 98.7 REMARK 620 5 HOH A 401 O 89.2 151.7 77.1 75.6 REMARK 620 6 HOH A 427 O 90.9 94.9 166.8 78.3 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD2 REMARK 620 2 HIS A 10 NE2 118.1 REMARK 620 3 ASP A 37 OD2 88.3 96.7 REMARK 620 4 BKP A 301 O1B 161.9 77.8 98.8 REMARK 620 5 HOH A 401 O 89.7 151.7 77.4 75.8 REMARK 620 6 HOH A 427 O 91.1 94.6 167.5 78.4 90.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 304 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 37 OD2 REMARK 620 2 ASN A 65 OD1 86.7 REMARK 620 3 HIS A 120 NE2 90.1 93.5 REMARK 620 4 HIS A 227 ND1 169.7 103.4 87.0 REMARK 620 5 BKP A 301 O2B 92.8 91.1 174.7 89.3 REMARK 620 6 HOH A 401 O 81.3 143.9 120.2 91.6 56.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 8 OD2 REMARK 620 2 HIS B 10 NE2 117.4 REMARK 620 3 ASP B 37 OD2 90.4 94.3 REMARK 620 4 HOH B 505 O 102.2 140.2 81.4 REMARK 620 5 HOH B 514 O 94.1 95.9 165.4 84.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 8 OD2 REMARK 620 2 HIS B 10 NE2 116.8 REMARK 620 3 ASP B 37 OD2 90.2 93.9 REMARK 620 4 BKP B 402 O1B 161.5 81.6 91.0 REMARK 620 5 HOH B 505 O 102.6 140.4 81.6 59.3 REMARK 620 6 HOH B 514 O 94.2 95.8 166.2 80.8 84.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 405 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 37 OD2 REMARK 620 2 ASN B 65 OD1 91.2 REMARK 620 3 HIS B 120 NE2 90.8 87.5 REMARK 620 4 HIS B 227 ND1 168.5 100.2 88.1 REMARK 620 5 BKP B 402 O2B 94.7 82.2 168.4 88.4 REMARK 620 6 HOH B 505 O 77.4 138.9 131.2 94.8 60.1 REMARK 620 N 1 2 3 4 5 DBREF 9OMC A 1 280 UNP P05637 APAH_ECOLI 1 280 DBREF 9OMC B 1 280 UNP P05637 APAH_ECOLI 1 280 SEQADV 9OMC HIS A 281 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS A 282 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS A 283 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS A 284 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS A 285 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS A 286 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS B 281 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS B 282 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS B 283 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS B 284 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS B 285 UNP P05637 EXPRESSION TAG SEQADV 9OMC HIS B 286 UNP P05637 EXPRESSION TAG SEQRES 1 A 286 MET ALA THR TYR LEU ILE GLY ASP VAL HIS GLY CYS TYR SEQRES 2 A 286 ASP GLU LEU ILE ALA LEU LEU HIS LYS VAL GLU PHE THR SEQRES 3 A 286 PRO GLY LYS ASP THR LEU TRP LEU THR GLY ASP LEU VAL SEQRES 4 A 286 ALA ARG GLY PRO GLY SER LEU ASP VAL LEU ARG TYR VAL SEQRES 5 A 286 LYS SER LEU GLY ASP SER VAL ARG LEU VAL LEU GLY ASN SEQRES 6 A 286 HIS ASP LEU HIS LEU LEU ALA VAL PHE ALA GLY ILE SER SEQRES 7 A 286 ARG ASN LYS PRO LYS ASP ARG LEU THR PRO LEU LEU GLU SEQRES 8 A 286 ALA PRO ASP ALA ASP GLU LEU LEU ASN TRP LEU ARG ARG SEQRES 9 A 286 GLN PRO LEU LEU GLN ILE ASP GLU GLU LYS LYS LEU VAL SEQRES 10 A 286 MET ALA HIS ALA GLY ILE THR PRO GLN TRP ASP LEU GLN SEQRES 11 A 286 THR ALA LYS GLU CYS ALA ARG ASP VAL GLU ALA VAL LEU SEQRES 12 A 286 SER SER ASP SER TYR PRO PHE PHE LEU ASP ALA MET TYR SEQRES 13 A 286 GLY ASP MET PRO ASN ASN TRP SER PRO GLU LEU ARG GLY SEQRES 14 A 286 LEU GLY ARG LEU ARG PHE ILE THR ASN ALA PHE THR ARG SEQRES 15 A 286 MET ARG PHE CYS PHE PRO ASN GLY GLN LEU ASP MET TYR SEQRES 16 A 286 SER LYS GLU SER PRO GLU GLU ALA PRO ALA PRO LEU LYS SEQRES 17 A 286 PRO TRP PHE ALA ILE PRO GLY PRO VAL ALA GLU GLU TYR SEQRES 18 A 286 SER ILE ALA PHE GLY HIS TRP ALA SER LEU GLU GLY LYS SEQRES 19 A 286 GLY THR PRO GLU GLY ILE TYR ALA LEU ASP THR GLY CYS SEQRES 20 A 286 CYS TRP GLY GLY THR LEU THR CYS LEU ARG TRP GLU ASP SEQRES 21 A 286 LYS GLN TYR PHE VAL GLN PRO SER ASN ARG HIS LYS ASP SEQRES 22 A 286 LEU GLY GLU ALA ALA ALA SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 286 MET ALA THR TYR LEU ILE GLY ASP VAL HIS GLY CYS TYR SEQRES 2 B 286 ASP GLU LEU ILE ALA LEU LEU HIS LYS VAL GLU PHE THR SEQRES 3 B 286 PRO GLY LYS ASP THR LEU TRP LEU THR GLY ASP LEU VAL SEQRES 4 B 286 ALA ARG GLY PRO GLY SER LEU ASP VAL LEU ARG TYR VAL SEQRES 5 B 286 LYS SER LEU GLY ASP SER VAL ARG LEU VAL LEU GLY ASN SEQRES 6 B 286 HIS ASP LEU HIS LEU LEU ALA VAL PHE ALA GLY ILE SER SEQRES 7 B 286 ARG ASN LYS PRO LYS ASP ARG LEU THR PRO LEU LEU GLU SEQRES 8 B 286 ALA PRO ASP ALA ASP GLU LEU LEU ASN TRP LEU ARG ARG SEQRES 9 B 286 GLN PRO LEU LEU GLN ILE ASP GLU GLU LYS LYS LEU VAL SEQRES 10 B 286 MET ALA HIS ALA GLY ILE THR PRO GLN TRP ASP LEU GLN SEQRES 11 B 286 THR ALA LYS GLU CYS ALA ARG ASP VAL GLU ALA VAL LEU SEQRES 12 B 286 SER SER ASP SER TYR PRO PHE PHE LEU ASP ALA MET TYR SEQRES 13 B 286 GLY ASP MET PRO ASN ASN TRP SER PRO GLU LEU ARG GLY SEQRES 14 B 286 LEU GLY ARG LEU ARG PHE ILE THR ASN ALA PHE THR ARG SEQRES 15 B 286 MET ARG PHE CYS PHE PRO ASN GLY GLN LEU ASP MET TYR SEQRES 16 B 286 SER LYS GLU SER PRO GLU GLU ALA PRO ALA PRO LEU LYS SEQRES 17 B 286 PRO TRP PHE ALA ILE PRO GLY PRO VAL ALA GLU GLU TYR SEQRES 18 B 286 SER ILE ALA PHE GLY HIS TRP ALA SER LEU GLU GLY LYS SEQRES 19 B 286 GLY THR PRO GLU GLY ILE TYR ALA LEU ASP THR GLY CYS SEQRES 20 B 286 CYS TRP GLY GLY THR LEU THR CYS LEU ARG TRP GLU ASP SEQRES 21 B 286 LYS GLN TYR PHE VAL GLN PRO SER ASN ARG HIS LYS ASP SEQRES 22 B 286 LEU GLY GLU ALA ALA ALA SER HIS HIS HIS HIS HIS HIS HET BKP A 301 36 HET MN A 302 1 HET MG A 303 1 HET MN A 304 1 HET EPE B 401 32 HET BKP B 402 36 HET MN B 403 1 HET MG B 404 1 HET MN B 405 1 HETNAM BKP 5'-O-[(S)-HYDROXY{[(S)-HYDROXY{[(R)- HETNAM 2 BKP HYDROXY(PHOSPHONOOXY) HETNAM 3 BKP PHOSPHORYL]OXY}PHOSPHORYL]OXY}PHOSPHORYL]GUANOSINE HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 BKP 2(C10 H17 N5 O17 P4) FORMUL 4 MN 4(MN 2+) FORMUL 5 MG 2(MG 2+) FORMUL 7 EPE C8 H18 N2 O4 S FORMUL 12 HOH *367(H2 O) HELIX 1 AA1 CYS A 12 VAL A 23 1 12 HELIX 2 AA2 GLY A 44 LEU A 55 1 12 HELIX 3 AA3 GLY A 64 ALA A 75 1 12 HELIX 4 AA4 LYS A 81 ARG A 85 5 5 HELIX 5 AA5 LEU A 86 GLU A 91 1 6 HELIX 6 AA6 ASP A 94 ARG A 103 1 10 HELIX 7 AA7 ASP A 128 SER A 144 1 17 HELIX 8 AA8 SER A 147 TYR A 156 1 10 HELIX 9 AA9 ARG A 168 ARG A 182 1 15 HELIX 10 AB1 SER A 199 ALA A 203 5 5 HELIX 11 AB2 PHE A 211 ILE A 213 5 3 HELIX 12 AB3 GLY A 215 TYR A 221 1 7 HELIX 13 AB4 TRP A 228 GLU A 232 5 5 HELIX 14 AB5 GLY A 246 GLY A 250 5 5 HELIX 15 AB6 CYS B 12 VAL B 23 1 12 HELIX 16 AB7 GLY B 44 LEU B 55 1 12 HELIX 17 AB8 GLY B 64 ALA B 75 1 12 HELIX 18 AB9 LYS B 81 ARG B 85 5 5 HELIX 19 AC1 LEU B 86 ALA B 92 1 7 HELIX 20 AC2 ASP B 94 ARG B 103 1 10 HELIX 21 AC3 ASP B 128 SER B 145 1 18 HELIX 22 AC4 SER B 147 TYR B 156 1 10 HELIX 23 AC5 ARG B 168 ARG B 182 1 15 HELIX 24 AC6 SER B 199 ALA B 203 5 5 HELIX 25 AC7 PHE B 211 ILE B 213 5 3 HELIX 26 AC8 GLY B 215 TYR B 221 1 7 HELIX 27 AC9 TRP B 228 GLU B 232 5 5 HELIX 28 AD1 GLY B 246 GLY B 250 5 5 SHEET 1 AA1 5 VAL A 59 LEU A 61 0 SHEET 2 AA1 5 THR A 31 LEU A 34 1 N LEU A 32 O ARG A 60 SHEET 3 AA1 5 THR A 3 ILE A 6 1 N TYR A 4 O TRP A 33 SHEET 4 AA1 5 THR A 252 ARG A 257 -1 O LEU A 256 N LEU A 5 SHEET 5 AA1 5 GLN A 262 PRO A 267 -1 O GLN A 262 N ARG A 257 SHEET 1 AA2 4 LEU A 108 ASP A 111 0 SHEET 2 AA2 4 LEU A 116 ALA A 119 -1 O LEU A 116 N ASP A 111 SHEET 3 AA2 4 SER A 222 PHE A 225 1 O ALA A 224 N VAL A 117 SHEET 4 AA2 4 ILE A 240 ALA A 242 1 O TYR A 241 N ILE A 223 SHEET 1 AA3 2 PHE A 185 CYS A 186 0 SHEET 2 AA3 2 LYS A 208 PRO A 209 -1 O LYS A 208 N CYS A 186 SHEET 1 AA4 5 VAL B 59 LEU B 61 0 SHEET 2 AA4 5 THR B 31 LEU B 34 1 N LEU B 32 O ARG B 60 SHEET 3 AA4 5 THR B 3 ILE B 6 1 N TYR B 4 O TRP B 33 SHEET 4 AA4 5 THR B 252 ARG B 257 -1 O LEU B 256 N LEU B 5 SHEET 5 AA4 5 GLN B 262 PRO B 267 -1 O GLN B 262 N ARG B 257 SHEET 1 AA5 4 LEU B 108 ASP B 111 0 SHEET 2 AA5 4 LEU B 116 ALA B 119 -1 O LEU B 116 N ASP B 111 SHEET 3 AA5 4 SER B 222 PHE B 225 1 O ALA B 224 N VAL B 117 SHEET 4 AA5 4 ILE B 240 ALA B 242 1 O TYR B 241 N ILE B 223 SHEET 1 AA6 2 PHE B 185 CYS B 186 0 SHEET 2 AA6 2 LYS B 208 PRO B 209 -1 O LYS B 208 N CYS B 186 LINK OD2 ASP A 8 MN A MN A 302 1555 1555 2.20 LINK OD2 ASP A 8 MG B MG A 303 1555 1555 2.20 LINK NE2 HIS A 10 MN A MN A 302 1555 1555 2.38 LINK NE2 HIS A 10 MG B MG A 303 1555 1555 2.39 LINK OD2 ASP A 37 MN A MN A 302 1555 1555 2.36 LINK OD2 ASP A 37 MG B MG A 303 1555 1555 2.36 LINK OD2 ASP A 37 MN MN A 304 1555 1555 2.28 LINK OD1 ASN A 65 MN MN A 304 1555 1555 2.14 LINK NE2 HIS A 120 MN MN A 304 1555 1555 2.17 LINK ND1 HIS A 227 MN MN A 304 1555 1555 2.29 LINK O1B BKP A 301 MN A MN A 302 1555 1555 2.72 LINK O1B BKP A 301 MG B MG A 303 1555 1555 2.71 LINK O2B BKP A 301 MN MN A 304 1555 1555 2.13 LINK MN A MN A 302 O HOH A 401 1555 1555 2.07 LINK MN A MN A 302 O HOH A 427 1555 1555 2.09 LINK MG B MG A 303 O HOH A 401 1555 1555 2.05 LINK MG B MG A 303 O HOH A 427 1555 1555 2.09 LINK MN MN A 304 O HOH A 401 1555 1555 1.95 LINK OD2 ASP B 8 MN A MN B 403 1555 1555 2.20 LINK OD2 ASP B 8 MG B MG B 404 1555 1555 2.20 LINK NE2 HIS B 10 MN A MN B 403 1555 1555 2.40 LINK NE2 HIS B 10 MG B MG B 404 1555 1555 2.41 LINK OD2 ASP B 37 MN A MN B 403 1555 1555 2.24 LINK OD2 ASP B 37 MG B MG B 404 1555 1555 2.25 LINK OD2 ASP B 37 MN MN B 405 1555 1555 2.36 LINK OD1 ASN B 65 MN MN B 405 1555 1555 2.12 LINK NE2 HIS B 120 MN MN B 405 1555 1555 2.16 LINK ND1 HIS B 227 MN MN B 405 1555 1555 2.21 LINK O1B BKP B 402 MG B MG B 404 1555 1555 2.82 LINK O2B BKP B 402 MN MN B 405 1555 1555 2.60 LINK MN A MN B 403 O HOH B 505 1555 1555 2.05 LINK MN A MN B 403 O HOH B 514 1555 1555 2.08 LINK MG B MG B 404 O HOH B 505 1555 1555 2.03 LINK MG B MG B 404 O HOH B 514 1555 1555 2.07 LINK MN MN B 405 O HOH B 505 1555 1555 2.12 CISPEP 1 MET A 159 PRO A 160 0 -3.88 CISPEP 2 ALA A 205 PRO A 206 0 -1.46 CISPEP 3 MET B 159 PRO B 160 0 -4.76 CISPEP 4 ALA B 205 PRO B 206 0 -3.33 CRYST1 165.755 54.562 119.447 90.00 129.47 90.00 C 1 2 1 8 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 0.006033 0.000000 0.004968 0.00000 SCALE2 0.000000 0.018328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010845 0.00000 CONECT 52 4240 4241 CONECT 69 4240 4241 CONECT 278 4240 4241 4242 CONECT 484 4242 CONECT 925 4242 CONECT 1762 4242 CONECT 2147 4311 4312 CONECT 2164 4311 4312 CONECT 2373 4311 4312 4313 CONECT 2579 4313 CONECT 3024 4313 CONECT 3864 4313 CONECT 4204 4205 4206 4207 4208 CONECT 4205 4204 4240 4241 CONECT 4206 4204 4242 CONECT 4207 4204 4233 CONECT 4208 4204 4209 CONECT 4209 4208 4210 4211 4212 CONECT 4210 4209 CONECT 4211 4209 CONECT 4212 4209 4213 CONECT 4213 4212 4214 CONECT 4214 4213 4215 4216 CONECT 4215 4214 4220 CONECT 4216 4214 4217 4218 CONECT 4217 4216 CONECT 4218 4216 4219 4220 CONECT 4219 4218 CONECT 4220 4215 4218 4221 CONECT 4221 4220 4222 4231 CONECT 4222 4221 4223 CONECT 4223 4222 4224 CONECT 4224 4223 4225 4231 CONECT 4225 4224 4226 4227 CONECT 4226 4225 CONECT 4227 4225 4228 CONECT 4228 4227 4229 4230 CONECT 4229 4228 CONECT 4230 4228 4231 CONECT 4231 4221 4224 4230 CONECT 4232 4236 4237 4238 4239 CONECT 4233 4207 4234 4235 4236 CONECT 4234 4233 CONECT 4235 4233 CONECT 4236 4232 4233 CONECT 4237 4232 CONECT 4238 4232 CONECT 4239 4232 CONECT 4240 52 69 278 4205 CONECT 4240 4314 4340 CONECT 4241 52 69 278 4205 CONECT 4241 4314 4340 CONECT 4242 278 484 925 1762 CONECT 4242 4206 4314 CONECT 4243 4244 4248 4252 CONECT 4244 4243 4245 4258 4259 CONECT 4245 4244 4246 4260 4261 CONECT 4246 4245 4247 4249 CONECT 4247 4246 4248 4262 4263 CONECT 4248 4243 4247 4264 4265 CONECT 4249 4246 4250 4266 4267 CONECT 4250 4249 4251 4268 4269 CONECT 4251 4250 4270 CONECT 4252 4243 4253 4271 4272 CONECT 4253 4252 4254 4273 4274 CONECT 4254 4253 4255 4256 4257 CONECT 4255 4254 CONECT 4256 4254 CONECT 4257 4254 CONECT 4258 4244 CONECT 4259 4244 CONECT 4260 4245 CONECT 4261 4245 CONECT 4262 4247 CONECT 4263 4247 CONECT 4264 4248 CONECT 4265 4248 CONECT 4266 4249 CONECT 4267 4249 CONECT 4268 4250 CONECT 4269 4250 CONECT 4270 4251 CONECT 4271 4252 CONECT 4272 4252 CONECT 4273 4253 CONECT 4274 4253 CONECT 4275 4276 4277 4278 4279 CONECT 4276 4275 4312 CONECT 4277 4275 4313 CONECT 4278 4275 4304 CONECT 4279 4275 4280 CONECT 4280 4279 4281 4282 4283 CONECT 4281 4280 CONECT 4282 4280 CONECT 4283 4280 4284 CONECT 4284 4283 4285 CONECT 4285 4284 4286 4287 CONECT 4286 4285 4291 CONECT 4287 4285 4288 4289 CONECT 4288 4287 CONECT 4289 4287 4290 4291 CONECT 4290 4289 CONECT 4291 4286 4289 4292 CONECT 4292 4291 4293 4302 CONECT 4293 4292 4294 CONECT 4294 4293 4295 CONECT 4295 4294 4296 4302 CONECT 4296 4295 4297 4298 CONECT 4297 4296 CONECT 4298 4296 4299 CONECT 4299 4298 4300 4301 CONECT 4300 4299 CONECT 4301 4299 4302 CONECT 4302 4292 4295 4301 CONECT 4303 4307 4308 4309 4310 CONECT 4304 4278 4305 4306 4307 CONECT 4305 4304 CONECT 4306 4304 CONECT 4307 4303 4304 CONECT 4308 4303 CONECT 4309 4303 CONECT 4310 4303 CONECT 4311 2147 2164 2373 4502 CONECT 4311 4511 CONECT 4312 2147 2164 2373 4276 CONECT 4312 4502 4511 CONECT 4313 2373 2579 3024 3864 CONECT 4313 4277 4502 CONECT 4314 4240 4241 4242 CONECT 4340 4240 4241 CONECT 4502 4311 4312 4313 CONECT 4511 4311 4312 MASTER 385 0 9 28 22 0 0 6 4661 2 132 44 END