HEADER HYDROLASE 07-MAY-25 9OJD TITLE CRYSTAL STRUCTURE OF E. COLI DIADENOSINE TETRAPHOSPHATE HYDROLASE TITLE 2 (APAH) 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 2 10-JUN-26 9OJD 1 JRNL REVDAT 1 03-SEP-25 9OJD 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. 1.77 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 82838 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.410 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 28.5600 - 4.2600 0.99 5935 151 0.1671 0.1761 REMARK 3 2 4.2600 - 3.3800 1.00 5860 140 0.1568 0.1644 REMARK 3 3 3.3800 - 2.9600 1.00 5796 145 0.1876 0.1949 REMARK 3 4 2.9500 - 2.6800 1.00 5810 146 0.1977 0.1966 REMARK 3 5 2.6800 - 2.4900 1.00 5790 144 0.1968 0.2464 REMARK 3 6 2.4900 - 2.3500 1.00 5802 146 0.1939 0.2190 REMARK 3 7 2.3500 - 2.2300 1.00 5791 137 0.1860 0.2007 REMARK 3 8 2.2300 - 2.1300 1.00 5756 148 0.1848 0.2063 REMARK 3 9 2.1300 - 2.0500 1.00 5770 145 0.1874 0.2224 REMARK 3 10 2.0500 - 1.9800 1.00 5770 149 0.1955 0.2142 REMARK 3 11 1.9800 - 1.9200 1.00 5768 129 0.2088 0.2362 REMARK 3 12 1.9200 - 1.8600 1.00 5803 147 0.2140 0.2541 REMARK 3 13 1.8600 - 1.8100 1.00 5745 146 0.2287 0.2695 REMARK 3 14 1.8100 - 1.7700 0.94 5442 127 0.2548 0.2944 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) : 0.196 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.773 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.91 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 : 0.007 4343 REMARK 3 ANGLE : 0.948 5924 REMARK 3 CHIRALITY : 0.058 637 REMARK 3 PLANARITY : 0.011 768 REMARK 3 DIHEDRAL : 15.197 595 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 : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 2 through 80 or REMARK 3 (resid 81 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 82 REMARK 3 through 96 or (resid 97 and (name N or REMARK 3 name CA or name C or name O or name CB or REMARK 3 name CG )) or resid 98 through 190 or REMARK 3 resid 192 through 219 or (resid 220 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB or name CG )) or resid 221 REMARK 3 through 270)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 2 through 78 or REMARK 3 (resid 79 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 80 REMARK 3 through 82 or (resid 83 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 84 through 136 or (resid 137 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 138 through 190 or REMARK 3 resid 192 through 200 or (resid 201 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 202 through 218 or REMARK 3 (resid 219 through 220 and (name N or REMARK 3 name CA or name C or name O or name CB or REMARK 3 name CG )) or resid 221 through 233 or REMARK 3 (resid 234 and (name N or name CA or name REMARK 3 C or name O or name CB or name CG )) or REMARK 3 resid 235 through 270)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9OJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000295669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-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) : 0.97930 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 : 82849 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 28.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 64.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CONDITIONS: 0.3 MM APAH (10 MG/ML), 1 REMARK 280 MM DTT, 10 MM MGCL2, 25 MM HEPES (PH 7.5), 0.2 M NACL. WELL REMARK 280 SOLUTION: 0.1 M BIS-TRIS (PH 6.5), 0.3 M SODIUM POTASSIUM REMARK 280 TARTRATE, 18% 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 83.88200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.61200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 83.88200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.61200 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 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 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 CG CD CE NZ 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 CD OE1 OE2 REMARK 470 LYS A 234 CD CE NZ REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 LYS B 83 CD CE NZ REMARK 470 GLU B 97 CD OE1 OE2 REMARK 470 GLU B 201 CD OE1 OE2 REMARK 470 GLU B 220 CD OE1 OE2 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 O HOH A 656 O HOH A 667 2.03 REMARK 500 O HOH A 547 O HOH A 651 2.08 REMARK 500 O HOH B 628 O HOH B 640 2.09 REMARK 500 O HOH A 540 O HOH A 593 2.14 REMARK 500 O HOH B 492 O HOH B 611 2.17 REMARK 500 O HOH A 622 O HOH A 665 2.17 REMARK 500 O HOH A 407 O HOH A 591 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 616 O HOH B 528 2555 2.04 REMARK 500 O HOH A 438 O HOH A 467 4555 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 40 148.80 83.87 REMARK 500 ARG A 41 -57.84 76.86 REMARK 500 ARG A 184 -70.73 -133.19 REMARK 500 HIS A 227 -54.82 70.53 REMARK 500 ALA B 40 151.16 83.32 REMARK 500 ARG B 41 -58.84 76.23 REMARK 500 ARG B 184 -70.85 -134.90 REMARK 500 HIS B 227 -54.50 70.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 104 0.12 SIDE CHAIN 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD2 REMARK 620 2 HIS A 10 NE2 118.9 REMARK 620 3 ASP A 37 OD2 89.3 92.9 REMARK 620 4 HOH A 442 O 97.2 94.6 166.2 REMARK 620 5 HOH A 597 O 114.8 125.9 82.0 84.3 REMARK 620 N 1 2 3 4 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 37 OD2 REMARK 620 2 ASN A 65 OD1 89.3 REMARK 620 3 HIS A 120 NE2 90.1 94.7 REMARK 620 4 HIS A 227 ND1 168.2 101.4 94.0 REMARK 620 5 HOH A 597 O 84.6 114.7 150.0 86.4 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 90.9 92.5 REMARK 620 4 HOH B 470 O 95.8 91.8 169.5 REMARK 620 5 HOH B 570 O 119.1 124.2 85.8 83.8 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 37 OD2 REMARK 620 2 ASN B 65 OD1 88.9 REMARK 620 3 HIS B 120 NE2 92.1 93.1 REMARK 620 4 HIS B 227 ND1 168.5 102.1 90.6 REMARK 620 5 HOH B 570 O 81.3 117.2 148.7 90.7 REMARK 620 N 1 2 3 4 DBREF 9OJD A 1 280 UNP P05637 APAH_ECOLI 1 280 DBREF 9OJD B 1 280 UNP P05637 APAH_ECOLI 1 280 SEQADV 9OJD HIS A 281 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS A 282 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS A 283 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS A 284 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS A 285 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS A 286 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS B 281 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS B 282 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS B 283 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS B 284 UNP P05637 EXPRESSION TAG SEQADV 9OJD HIS B 285 UNP P05637 EXPRESSION TAG SEQADV 9OJD 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 MN A 301 1 HET MG A 302 1 HET EPE B 301 32 HET MN B 302 1 HET MG B 303 1 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 MN 2(MN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 8 HOH *525(H2 O) HELIX 1 AA1 CYS A 12 VAL A 23 1 12 HELIX 2 AA2 GLY A 44 GLY A 56 1 13 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 PHE A 211 ILE A 213 5 3 HELIX 11 AB2 GLY A 215 TYR A 221 1 7 HELIX 12 AB3 TRP A 228 GLU A 232 5 5 HELIX 13 AB4 GLY A 246 GLY A 250 5 5 HELIX 14 AB5 CYS B 12 VAL B 23 1 12 HELIX 15 AB6 GLY B 44 LEU B 55 1 12 HELIX 16 AB7 GLY B 64 ALA B 75 1 12 HELIX 17 AB8 LYS B 81 ARG B 85 5 5 HELIX 18 AB9 LEU B 86 GLU B 91 1 6 HELIX 19 AC1 ASP B 94 ARG B 103 1 10 HELIX 20 AC2 ASP B 128 SER B 144 1 17 HELIX 21 AC3 SER B 147 TYR B 156 1 10 HELIX 22 AC4 ARG B 168 ARG B 182 1 15 HELIX 23 AC5 SER B 199 ALA B 203 5 5 HELIX 24 AC6 PHE B 211 ILE B 213 5 3 HELIX 25 AC7 GLY B 215 TYR B 221 1 7 HELIX 26 AC8 TRP B 228 GLU B 232 5 5 HELIX 27 AC9 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 3 LEU A 192 ASP A 193 0 SHEET 2 AA3 3 PHE A 185 CYS A 186 -1 N PHE A 185 O ASP A 193 SHEET 3 AA3 3 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 3 LEU B 192 ASP B 193 0 SHEET 2 AA6 3 PHE B 185 CYS B 186 -1 N PHE B 185 O ASP B 193 SHEET 3 AA6 3 LYS B 208 PRO B 209 -1 O LYS B 208 N CYS B 186 LINK OD2 ASP A 8 MG MG A 302 1555 1555 2.26 LINK NE2 HIS A 10 MG MG A 302 1555 1555 2.39 LINK OD2 ASP A 37 MN MN A 301 1555 1555 2.34 LINK OD2 ASP A 37 MG MG A 302 1555 1555 2.28 LINK OD1 ASN A 65 MN MN A 301 1555 1555 2.13 LINK NE2 HIS A 120 MN MN A 301 1555 1555 2.14 LINK ND1 HIS A 227 MN MN A 301 1555 1555 2.31 LINK MN MN A 301 O HOH A 597 1555 1555 2.24 LINK MG MG A 302 O HOH A 442 1555 1555 2.25 LINK MG MG A 302 O HOH A 597 1555 1555 2.42 LINK OD2 ASP B 8 MG MG B 303 1555 1555 2.29 LINK NE2 HIS B 10 MG MG B 303 1555 1555 2.47 LINK OD2 ASP B 37 MN MN B 302 1555 1555 2.33 LINK OD2 ASP B 37 MG MG B 303 1555 1555 2.19 LINK OD1 ASN B 65 MN MN B 302 1555 1555 2.14 LINK NE2 HIS B 120 MN MN B 302 1555 1555 2.14 LINK ND1 HIS B 227 MN MN B 302 1555 1555 2.20 LINK MN MN B 302 O HOH B 570 1555 1555 2.41 LINK MG MG B 303 O HOH B 470 1555 1555 2.19 LINK MG MG B 303 O HOH B 570 1555 1555 2.34 CISPEP 1 MET A 159 PRO A 160 0 -0.15 CISPEP 2 ALA A 205 PRO A 206 0 0.42 CISPEP 3 MET B 159 PRO B 160 0 0.68 CISPEP 4 ALA B 205 PRO B 206 0 1.55 CRYST1 167.764 55.224 120.388 90.00 129.57 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 0.005961 0.000000 0.004926 0.00000 SCALE2 0.000000 0.018108 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010776 0.00000 MTRIX1 1 -0.022113 -0.051299 0.998438 3.53129 1 MTRIX2 1 0.035519 -0.998093 -0.050495 -27.86179 1 MTRIX3 1 0.999124 0.034347 0.023893 5.02362 1 CONECT 52 4211 CONECT 69 4211 CONECT 278 4210 4211 CONECT 484 4210 CONECT 924 4210 CONECT 1759 4210 CONECT 2147 4245 CONECT 2164 4245 CONECT 2373 4244 4245 CONECT 2579 4244 CONECT 3019 4244 CONECT 3870 4244 CONECT 4210 278 484 924 1759 CONECT 4210 4442 CONECT 4211 52 69 278 4287 CONECT 4211 4442 CONECT 4212 4213 4217 4221 CONECT 4213 4212 4214 4227 4228 CONECT 4214 4213 4215 4229 4230 CONECT 4215 4214 4216 4218 CONECT 4216 4215 4217 4231 4232 CONECT 4217 4212 4216 4233 4234 CONECT 4218 4215 4219 4235 4236 CONECT 4219 4218 4220 4237 4238 CONECT 4220 4219 4239 CONECT 4221 4212 4222 4240 4241 CONECT 4222 4221 4223 4242 4243 CONECT 4223 4222 4224 4225 4226 CONECT 4224 4223 CONECT 4225 4223 CONECT 4226 4223 CONECT 4227 4213 CONECT 4228 4213 CONECT 4229 4214 CONECT 4230 4214 CONECT 4231 4216 CONECT 4232 4216 CONECT 4233 4217 CONECT 4234 4217 CONECT 4235 4218 CONECT 4236 4218 CONECT 4237 4219 CONECT 4238 4219 CONECT 4239 4220 CONECT 4240 4221 CONECT 4241 4221 CONECT 4242 4222 CONECT 4243 4222 CONECT 4244 2373 2579 3019 3870 CONECT 4244 4684 CONECT 4245 2147 2164 2373 4584 CONECT 4245 4684 CONECT 4287 4211 CONECT 4442 4210 4211 CONECT 4584 4245 CONECT 4684 4244 4245 MASTER 429 0 5 27 24 0 0 9 4742 2 56 44 END