HEADER HYDROLASE 15-MAY-25 9OND TITLE CRYSTAL STRUCTURE OF E. COLI APAH IN COMPLEX WITH PPAGG 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA PPAGG; COMPND 10 CHAIN: D, E; COMPND 11 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; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS APAH, SYMMETRICAL HYDROLASE, RNA DECAPPING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.NUTHANAKANTI,A.SERGANOV REVDAT 2 10-JUN-26 9OND 1 JRNL REVDAT 1 03-SEP-25 9OND 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. V. 22 895 2026 JRNL REFN ESSN 1552-4469 JRNL PMID 40789943 JRNL DOI 10.1038/S41589-025-01991-4 REMARK 2 REMARK 2 RESOLUTION. 2.16 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) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 43717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2180 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 82.8800 - 5.4400 0.95 2643 138 0.1797 0.1888 REMARK 3 2 5.4400 - 4.3200 0.95 2586 150 0.1556 0.1680 REMARK 3 3 4.3100 - 3.7700 0.94 2512 148 0.1636 0.2213 REMARK 3 4 3.7700 - 3.4200 0.93 2504 135 0.1781 0.2436 REMARK 3 5 3.4200 - 3.1800 0.94 2534 134 0.2094 0.2775 REMARK 3 6 3.1800 - 2.9900 0.96 2605 113 0.2130 0.2674 REMARK 3 7 2.9900 - 2.8400 0.97 2605 123 0.2055 0.2891 REMARK 3 8 2.8400 - 2.7200 0.98 2639 108 0.2090 0.2381 REMARK 3 9 2.7200 - 2.6100 0.98 2611 150 0.2109 0.2346 REMARK 3 10 2.6100 - 2.5200 0.99 2657 128 0.2068 0.2644 REMARK 3 11 2.5200 - 2.4400 0.99 2645 145 0.2284 0.2742 REMARK 3 12 2.4400 - 2.3700 0.99 2570 166 0.2361 0.2867 REMARK 3 13 2.3700 - 2.3100 0.99 2625 152 0.2510 0.2881 REMARK 3 14 2.3100 - 2.2600 0.98 2655 122 0.2653 0.2785 REMARK 3 15 2.2600 - 2.2000 0.98 2573 127 0.2828 0.3229 REMARK 3 16 2.2000 - 2.1600 0.96 2573 141 0.2963 0.3441 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.009 4414 REMARK 3 ANGLE : 1.031 6034 REMARK 3 CHIRALITY : 0.056 647 REMARK 3 PLANARITY : 0.009 771 REMARK 3 DIHEDRAL : 19.350 605 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 9OND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000295930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-22 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-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43891 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 92.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 1.15400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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 (%): 63.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CONDITIONS: 0.3 MM APAH (10 MG/ML), 1 REMARK 280 MM DTT, 0.7 MM PPAGG, 4 MM MGCL2, 10 MM CA(OAC)2, 25 MM HEPES REMARK 280 (PH 7.5), 0.2 M NACL. WELL SOLUTION: 0.2 M TRISODIUM CITRATE, 20% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING DROP, 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 83.16600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.41200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 83.16600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.41200 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 G D 3 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 465 G E 3 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 NE CZ NH1 NH2 REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 201 CG CD OE1 OE2 REMARK 470 GLU A 219 CG CD OE1 OE2 REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 ARG A 270 CG CD NE CZ NH1 NH2 REMARK 470 G D 2 O4' C3' O3' C2' O2' C1' N9 REMARK 470 G D 2 C8 N7 C5 C6 O6 N1 C2 REMARK 470 G D 2 N2 N3 C4 REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 LYS B 83 CE NZ REMARK 470 GLU B 202 CG CD OE1 OE2 REMARK 470 LYS B 208 CD CE NZ REMARK 470 LYS B 234 CG CD CE NZ REMARK 470 GLU B 238 CG CD OE1 OE2 REMARK 470 G E 2 C5' C4' O4' C3' O3' C2' O2' REMARK 470 G E 2 C1' N9 C8 N7 C5 C6 O6 REMARK 470 G E 2 N1 C2 N2 N3 C4 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 G D 2 O3' - P - O5' ANGL. DEV. = 11.5 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 ALA A 40 143.65 82.10 REMARK 500 ARG A 41 -57.14 80.81 REMARK 500 ARG A 184 -77.00 -138.80 REMARK 500 PRO A 206 30.04 -92.72 REMARK 500 HIS A 227 -50.38 69.79 REMARK 500 ASN A 269 5.92 -68.43 REMARK 500 ALA B 40 147.85 82.65 REMARK 500 ARG B 41 -57.43 79.20 REMARK 500 ARG B 85 30.40 71.80 REMARK 500 ARG B 184 -76.74 -136.25 REMARK 500 HIS B 227 -51.66 70.07 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 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD2 REMARK 620 2 HIS A 10 NE2 115.5 REMARK 620 3 ASP A 37 OD2 87.9 89.3 REMARK 620 4 HOH D 101 O 119.6 123.1 79.9 REMARK 620 5 HOH D 102 O 98.5 89.1 173.4 95.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD2 REMARK 620 2 HIS A 10 NE2 115.9 REMARK 620 3 ASP A 37 OD2 88.4 89.4 REMARK 620 4 HOH D 101 O 119.9 122.6 79.9 REMARK 620 5 HOH D 102 O 98.6 88.8 172.8 95.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 303 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 37 OD2 REMARK 620 2 ASN A 65 OD1 85.8 REMARK 620 3 HIS A 120 NE2 96.3 92.5 REMARK 620 4 HIS A 227 ND1 168.9 104.0 88.8 REMARK 620 5 HOH D 101 O 78.7 117.1 149.3 91.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 8 OD2 REMARK 620 2 HIS B 10 NE2 115.8 REMARK 620 3 ASP B 37 OD2 93.3 93.8 REMARK 620 4 HOH E 102 O 119.5 124.7 81.6 REMARK 620 5 HOH E 103 O 96.0 85.7 170.0 90.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 8 OD2 REMARK 620 2 HIS B 10 NE2 116.7 REMARK 620 3 ASP B 37 OD2 92.4 98.1 REMARK 620 4 HOH E 102 O 114.8 128.5 82.1 REMARK 620 5 HOH E 103 O 92.4 87.1 170.5 88.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 304 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 37 OD2 REMARK 620 2 ASN B 65 OD1 87.1 REMARK 620 3 HIS B 120 NE2 92.5 90.8 REMARK 620 4 HIS B 227 ND1 169.6 103.0 90.0 REMARK 620 5 HOH E 102 O 81.7 120.7 147.4 90.7 REMARK 620 N 1 2 3 4 DBREF 9OND A 1 280 UNP P05637 APAH_ECOLI 1 280 DBREF 9OND D 1 3 PDB 9OND 9OND 1 3 DBREF 9OND B 1 280 UNP P05637 APAH_ECOLI 1 280 DBREF 9OND E 1 3 PDB 9OND 9OND 1 3 SEQADV 9OND HIS A 281 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS A 282 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS A 283 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS A 284 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS A 285 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS A 286 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS B 281 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS B 282 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS B 283 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS B 284 UNP P05637 EXPRESSION TAG SEQADV 9OND HIS B 285 UNP P05637 EXPRESSION TAG SEQADV 9OND 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 D 3 ADP G G 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 SEQRES 1 E 3 ADP G G HET ADP D 1 38 HET ADP E 1 38 HET MN A 301 1 HET MG A 302 1 HET MN A 303 1 HET EPE B 301 32 HET MN B 302 1 HET MG B 303 1 HET MN B 304 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 MN 4(MN 2+) FORMUL 6 MG 2(MG 2+) FORMUL 8 EPE C8 H18 N2 O4 S FORMUL 12 HOH *261(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 144 1 17 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 PHE A 264 N CYS A 255 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 SER A 222 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 O3' ADP D 1 P G D 2 1555 1555 1.59 LINK O3' ADP E 1 P G E 2 1555 1555 1.60 LINK OD2 ASP A 8 MN A MN A 301 1555 1555 2.36 LINK OD2 ASP A 8 MG B MG A 302 1555 1555 2.35 LINK NE2 HIS A 10 MN A MN A 301 1555 1555 2.54 LINK NE2 HIS A 10 MG B MG A 302 1555 1555 2.54 LINK OD2 ASP A 37 MN A MN A 301 1555 1555 2.46 LINK OD2 ASP A 37 MG B MG A 302 1555 1555 2.45 LINK OD2 ASP A 37 MN MN A 303 1555 1555 2.35 LINK OD1 ASN A 65 MN MN A 303 1555 1555 2.23 LINK NE2 HIS A 120 MN MN A 303 1555 1555 2.15 LINK ND1 HIS A 227 MN MN A 303 1555 1555 2.31 LINK MN A MN A 301 O HOH D 101 1555 1555 2.04 LINK MN A MN A 301 O HOH D 102 1555 1555 2.23 LINK MG B MG A 302 O HOH D 101 1555 1555 2.05 LINK MG B MG A 302 O HOH D 102 1555 1555 2.23 LINK MN MN A 303 O HOH D 101 1555 1555 2.24 LINK OD2 ASP B 8 MN A MN B 302 1555 1555 2.33 LINK OD2 ASP B 8 MG B MG B 303 1555 1555 2.41 LINK NE2 HIS B 10 MN A MN B 302 1555 1555 2.54 LINK NE2 HIS B 10 MG B MG B 303 1555 1555 2.43 LINK OD2 ASP B 37 MN A MN B 302 1555 1555 2.35 LINK OD2 ASP B 37 MG B MG B 303 1555 1555 2.29 LINK OD2 ASP B 37 MN MN B 304 1555 1555 2.25 LINK OD1 ASN B 65 MN MN B 304 1555 1555 2.17 LINK NE2 HIS B 120 MN MN B 304 1555 1555 2.18 LINK ND1 HIS B 227 MN MN B 304 1555 1555 2.22 LINK MN A MN B 302 O HOH E 102 1555 1555 2.21 LINK MN A MN B 302 O HOH E 103 1555 1555 2.32 LINK MG B MG B 303 O HOH E 102 1555 1555 2.24 LINK MG B MG B 303 O HOH E 103 1555 1555 2.37 LINK MN MN B 304 O HOH E 102 1555 1555 2.30 CISPEP 1 MET A 159 PRO A 160 0 -3.53 CISPEP 2 ALA A 205 PRO A 206 0 -0.11 CISPEP 3 MET B 159 PRO B 160 0 -5.09 CISPEP 4 ALA B 205 PRO B 206 0 -2.51 CRYST1 166.332 54.824 119.172 90.00 129.28 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 0.006012 0.000000 0.004917 0.00000 SCALE2 0.000000 0.018240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010841 0.00000 CONECT 52 4301 4302 CONECT 69 4301 4302 CONECT 278 4301 4302 4303 CONECT 484 4303 CONECT 930 4303 CONECT 1764 4303 CONECT 2098 2099 2100 2101 2105 CONECT 2099 2098 CONECT 2100 2098 CONECT 2101 2098 CONECT 2102 2103 2104 2105 2106 CONECT 2103 2102 CONECT 2104 2102 CONECT 2105 2098 2102 CONECT 2106 2102 2107 CONECT 2107 2106 2108 2125 2126 CONECT 2108 2107 2109 2110 2127 CONECT 2109 2108 2114 CONECT 2110 2108 2111 2112 2128 CONECT 2111 2110 2136 CONECT 2112 2110 2113 2114 2129 CONECT 2113 2112 2130 CONECT 2114 2109 2112 2115 2131 CONECT 2115 2114 2116 2124 CONECT 2116 2115 2117 2132 CONECT 2117 2116 2118 CONECT 2118 2117 2119 2124 CONECT 2119 2118 2120 2121 CONECT 2120 2119 2133 2134 CONECT 2121 2119 2122 CONECT 2122 2121 2123 2135 CONECT 2123 2122 2124 CONECT 2124 2115 2118 2123 CONECT 2125 2107 CONECT 2126 2107 CONECT 2127 2108 CONECT 2128 2110 CONECT 2129 2112 CONECT 2130 2113 CONECT 2131 2114 CONECT 2132 2116 CONECT 2133 2120 CONECT 2134 2120 CONECT 2135 2122 CONECT 2136 2111 CONECT 2194 4336 4337 CONECT 2211 4336 4337 CONECT 2420 4336 4337 4338 CONECT 2626 4338 CONECT 3081 4338 CONECT 3922 4338 CONECT 4258 4259 4260 4261 4265 CONECT 4259 4258 CONECT 4260 4258 CONECT 4261 4258 CONECT 4262 4263 4264 4265 4266 CONECT 4263 4262 CONECT 4264 4262 CONECT 4265 4258 4262 CONECT 4266 4262 4267 CONECT 4267 4266 4268 4285 4286 CONECT 4268 4267 4269 4270 4287 CONECT 4269 4268 4274 CONECT 4270 4268 4271 4272 4288 CONECT 4271 4270 4296 CONECT 4272 4270 4273 4274 4289 CONECT 4273 4272 4290 CONECT 4274 4269 4272 4275 4291 CONECT 4275 4274 4276 4284 CONECT 4276 4275 4277 4292 CONECT 4277 4276 4278 CONECT 4278 4277 4279 4284 CONECT 4279 4278 4280 4281 CONECT 4280 4279 4293 4294 CONECT 4281 4279 4282 CONECT 4282 4281 4283 4295 CONECT 4283 4282 4284 CONECT 4284 4275 4278 4283 CONECT 4285 4267 CONECT 4286 4267 CONECT 4287 4268 CONECT 4288 4270 CONECT 4289 4272 CONECT 4290 4273 CONECT 4291 4274 CONECT 4292 4276 CONECT 4293 4280 CONECT 4294 4280 CONECT 4295 4282 CONECT 4296 4271 CONECT 4301 52 69 278 4465 CONECT 4301 4466 CONECT 4302 52 69 278 4465 CONECT 4302 4466 CONECT 4303 278 484 930 1764 CONECT 4303 4465 CONECT 4304 4305 4309 4313 CONECT 4305 4304 4306 4319 4320 CONECT 4306 4305 4307 4321 4322 CONECT 4307 4306 4308 4310 CONECT 4308 4307 4309 4323 4324 CONECT 4309 4304 4308 4325 4326 CONECT 4310 4307 4311 4327 4328 CONECT 4311 4310 4312 4329 4330 CONECT 4312 4311 4331 CONECT 4313 4304 4314 4332 4333 CONECT 4314 4313 4315 4334 4335 CONECT 4315 4314 4316 4317 4318 CONECT 4316 4315 CONECT 4317 4315 CONECT 4318 4315 CONECT 4319 4305 CONECT 4320 4305 CONECT 4321 4306 CONECT 4322 4306 CONECT 4323 4308 CONECT 4324 4308 CONECT 4325 4309 CONECT 4326 4309 CONECT 4327 4310 CONECT 4328 4310 CONECT 4329 4311 CONECT 4330 4311 CONECT 4331 4312 CONECT 4332 4313 CONECT 4333 4313 CONECT 4334 4314 CONECT 4335 4314 CONECT 4336 2194 2211 2420 4597 CONECT 4336 4598 CONECT 4337 2194 2211 2420 4597 CONECT 4337 4598 CONECT 4338 2420 2626 3081 3922 CONECT 4338 4597 CONECT 4465 4301 4302 4303 CONECT 4466 4301 4302 CONECT 4597 4336 4337 4338 CONECT 4598 4336 4337 MASTER 391 0 9 28 22 0 0 6 4545 4 138 46 END