HEADER HYDROLASE/RNA 23-JAN-15 4S2Y TITLE STRUCTURE OF E. COLI RPPH BOUND TO RNA AND THREE MAGNESIUM IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA PYROPHOSPHOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: (DI)NUCLEOSIDE POLYPHOSPHATE HYDROLASE, AP5A COMPND 5 PYROPHOSPHATASE; COMPND 6 EC: 3.6.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA (5'-R(*(APC)*GP*U)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: RPPH, NUDH, YGDP, B2830, JW2798; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: PREPARED BY IN VITRO TRANSCRIPTION KEYWDS NUDIX HYDROLASE, RNA PYROPHOSPHOHYDROLASE, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.VASILYEV,A.SERGANOV REVDAT 4 20-SEP-23 4S2Y 1 REMARK SEQADV LINK REVDAT 3 06-MAY-15 4S2Y 1 JRNL REVDAT 2 25-FEB-15 4S2Y 1 JRNL REVDAT 1 11-FEB-15 4S2Y 0 JRNL AUTH N.VASILYEV,A.SERGANOV JRNL TITL STRUCTURES OF RNA COMPLEXES WITH THE ESCHERICHIA COLI RNA JRNL TITL 2 PYROPHOSPHOHYDROLASE RPPH UNVEIL THE BASIS FOR SPECIFIC JRNL TITL 3 5'-END-DEPENDENT MRNA DECAY. JRNL REF J.BIOL.CHEM. V. 290 9487 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 25657011 JRNL DOI 10.1074/JBC.M114.634824 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 21062 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1054 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 19.4524 - 3.1964 1.00 2666 141 0.1508 0.1756 REMARK 3 2 3.1964 - 2.5388 0.99 2581 136 0.1726 0.1737 REMARK 3 3 2.5388 - 2.2184 0.99 2552 134 0.1763 0.2222 REMARK 3 4 2.2184 - 2.0158 0.98 2521 133 0.1658 0.1885 REMARK 3 5 2.0158 - 1.8715 0.97 2487 131 0.1837 0.2392 REMARK 3 6 1.8715 - 1.7612 0.96 2451 129 0.2023 0.2561 REMARK 3 7 1.7612 - 1.6730 0.96 2467 130 0.2180 0.2407 REMARK 3 8 1.6730 - 1.6003 0.90 2283 120 0.2645 0.3074 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.310 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 : 0.007 1429 REMARK 3 ANGLE : 1.016 1949 REMARK 3 CHIRALITY : 0.046 199 REMARK 3 PLANARITY : 0.005 241 REMARK 3 DIHEDRAL : 18.616 534 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' REMARK 3 ORIGIN FOR THE GROUP (A): 14.7568 -0.4097 11.7030 REMARK 3 T TENSOR REMARK 3 T11: 0.1773 T22: 0.1682 REMARK 3 T33: 0.1406 T12: -0.0125 REMARK 3 T13: -0.0124 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 2.6055 L22: 1.9732 REMARK 3 L33: 2.0301 L12: 0.2860 REMARK 3 L13: 0.0789 L23: -0.3279 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: -0.2974 S13: 0.0116 REMARK 3 S21: 0.2763 S22: -0.0261 S23: -0.1129 REMARK 3 S31: -0.1804 S32: 0.1570 S33: 0.0217 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): 25.7226 -0.9705 15.2259 REMARK 3 T TENSOR REMARK 3 T11: 0.3091 T22: 0.4699 REMARK 3 T33: 0.2518 T12: -0.0494 REMARK 3 T13: -0.0754 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 0.0027 L22: 0.0440 REMARK 3 L33: 0.0146 L12: -0.0099 REMARK 3 L13: 0.0054 L23: -0.0249 REMARK 3 S TENSOR REMARK 3 S11: -0.0174 S12: -0.0323 S13: 0.0553 REMARK 3 S21: 0.0416 S22: 0.0098 S23: -0.0309 REMARK 3 S31: 0.0170 S32: 0.0209 S33: -0.0062 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 4S2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000088113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21065 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.64300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.710 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4S2W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL GROWTH: 0.4 M AMMONIUM REMARK 280 SULFATE, 12% PEG 3350, 10% GLYCEROL. CRYSTAL SOAKING AND CROSS- REMARK 280 LINKING: 0.02 M SODIUM ACETATE PH 5.0, 0.2 SODIUM SULFATE, 15% REMARK 280 PEG 3350, 15% GLYCEROL. CRYSTAL SOAKING AND CRYOPROTECTION: 0.05 REMARK 280 M MOPS-NA PH 7.0, 0.025 M MAGNESIUM CHLORIDE, 15% PEG 3350, 25% REMARK 280 PENTAERYTHRITOL PROPOXYLATE 5/4 PO/OH, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K 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 39.81550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.24200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.81550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.24200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 1 REMARK 465 TRP A 87 REMARK 465 ASP A 88 REMARK 465 THR A 89 REMARK 465 LYS A 90 REMARK 465 PRO A 91 REMARK 465 U B 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 82 CG CD CE NZ REMARK 470 ARG A 83 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 135 CD NE CZ NH1 NH2 REMARK 470 APC B 1 N9 C8 N7 C5 C6 N6 N1 REMARK 470 APC B 1 C2 N3 C4 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 O2 SO4 A 204 O HOH A 398 2.15 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 ASN A 18 -163.64 -117.50 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 38 O REMARK 620 2 GLU A 58 OE2 93.2 REMARK 620 3 GLU A 121 OE2 173.0 85.9 REMARK 620 4 HOH A 310 O 89.0 95.7 84.2 REMARK 620 5 APC B 1 O1B 92.7 87.8 94.2 176.0 REMARK 620 6 APC B 1 O2A 91.5 169.0 90.6 94.4 82.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 54 OE1 REMARK 620 2 GLU A 58 OE2 88.1 REMARK 620 3 GLU A 121 OE1 169.3 84.8 REMARK 620 4 HOH A 308 O 89.2 110.5 85.9 REMARK 620 5 APC B 1 O1B 100.4 76.5 85.7 168.5 REMARK 620 6 HOH B 201 O 98.7 162.7 90.4 85.7 86.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 54 OE2 REMARK 620 2 HOH A 314 O 85.3 REMARK 620 3 HOH A 316 O 86.5 99.9 REMARK 620 4 APC B 1 O2B 101.9 97.9 161.0 REMARK 620 5 HOH B 201 O 97.0 177.7 79.8 82.2 REMARK 620 6 HOH B 202 O 165.0 84.6 84.5 90.4 93.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4S2V RELATED DB: PDB REMARK 900 RELATED ID: 4S2W RELATED DB: PDB REMARK 900 RELATED ID: 4S2X RELATED DB: PDB DBREF 4S2Y A 2 161 UNP P0A776 RPPH_ECOLI 1 160 DBREF 4S2Y B 1 3 PDB 4S2Y 4S2Y 1 3 SEQADV 4S2Y SER A 1 UNP P0A776 EXPRESSION TAG SEQADV 4S2Y ALA A 160 UNP P0A776 GLN 159 ENGINEERED MUTATION SEQADV 4S2Y ALA A 161 UNP P0A776 GLU 160 ENGINEERED MUTATION SEQRES 1 A 161 SER MET ILE ASP ASP ASP GLY TYR ARG PRO ASN VAL GLY SEQRES 2 A 161 ILE VAL ILE CYS ASN ARG GLN GLY GLN VAL MET TRP ALA SEQRES 3 A 161 ARG ARG PHE GLY GLN HIS SER TRP GLN PHE PRO GLN GLY SEQRES 4 A 161 GLY ILE ASN PRO GLY GLU SER ALA GLU GLN ALA MET TYR SEQRES 5 A 161 ARG GLU LEU PHE GLU GLU VAL GLY LEU SER ARG LYS ASP SEQRES 6 A 161 VAL ARG ILE LEU ALA SER THR ARG ASN TRP LEU ARG TYR SEQRES 7 A 161 LYS LEU PRO LYS ARG LEU VAL ARG TRP ASP THR LYS PRO SEQRES 8 A 161 VAL CYS ILE GLY GLN LYS GLN LYS TRP PHE LEU LEU GLN SEQRES 9 A 161 LEU VAL SER GLY ASP ALA GLU ILE ASN MET GLN THR SER SEQRES 10 A 161 SER THR PRO GLU PHE ASP GLY TRP ARG TRP VAL SER TYR SEQRES 11 A 161 TRP TYR PRO VAL ARG GLN VAL VAL SER PHE LYS ARG ASP SEQRES 12 A 161 VAL TYR ARG ARG VAL MET LYS GLU PHE ALA SER VAL VAL SEQRES 13 A 161 MET SER LEU ALA ALA SEQRES 1 B 3 APC G U HET APC B 1 21 HET MG A 201 1 HET MG A 202 1 HET CL A 203 1 HET SO4 A 204 5 HET MG B 101 1 HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE FORMUL 2 APC C11 H18 N5 O12 P3 FORMUL 3 MG 3(MG 2+) FORMUL 5 CL CL 1- FORMUL 6 SO4 O4 S 2- FORMUL 8 HOH *119(H2 O) HELIX 1 1 SER A 46 GLY A 60 1 15 HELIX 2 2 SER A 62 LYS A 64 5 3 HELIX 3 3 PRO A 81 VAL A 85 5 5 HELIX 4 4 GLY A 108 ILE A 112 5 5 HELIX 5 5 TYR A 132 VAL A 137 1 6 HELIX 6 6 VAL A 138 PHE A 140 5 3 HELIX 7 7 LYS A 141 ALA A 161 1 21 SHEET 1 A 4 GLN A 38 GLY A 40 0 SHEET 2 A 4 TYR A 8 CYS A 17 -1 N VAL A 12 O GLY A 39 SHEET 3 A 4 GLY A 95 LEU A 105 1 O LEU A 103 N VAL A 15 SHEET 4 A 4 VAL A 66 SER A 71 -1 N LEU A 69 O LEU A 102 SHEET 1 B 4 GLN A 38 GLY A 40 0 SHEET 2 B 4 TYR A 8 CYS A 17 -1 N VAL A 12 O GLY A 39 SHEET 3 B 4 GLY A 95 LEU A 105 1 O LEU A 103 N VAL A 15 SHEET 4 B 4 LEU A 76 LYS A 79 -1 N LEU A 76 O GLN A 98 SHEET 1 C 3 TRP A 34 GLN A 35 0 SHEET 2 C 3 GLN A 22 ARG A 28 -1 N ALA A 26 O GLN A 35 SHEET 3 C 3 PHE A 122 SER A 129 -1 O ASP A 123 N ARG A 27 LINK O3' APC B 1 P G B 2 1555 1555 1.61 LINK O GLN A 38 MG MG A 202 1555 1555 2.02 LINK OE1 GLU A 54 MG MG A 201 1555 1555 2.05 LINK OE2 GLU A 54 MG MG B 101 1555 1555 2.10 LINK OE2 GLU A 58 MG MG A 201 1555 1555 2.13 LINK OE2 GLU A 58 MG MG A 202 1555 1555 2.05 LINK OE1 GLU A 121 MG MG A 201 1555 1555 2.15 LINK OE2 GLU A 121 MG MG A 202 1555 1555 2.03 LINK MG MG A 201 O HOH A 308 1555 1555 2.09 LINK MG MG A 201 O1B APC B 1 1555 1555 2.31 LINK MG MG A 201 O HOH B 201 1555 1555 2.20 LINK MG MG A 202 O HOH A 310 1555 1555 2.13 LINK MG MG A 202 O1B APC B 1 1555 1555 1.92 LINK MG MG A 202 O2A APC B 1 1555 1555 2.03 LINK O HOH A 314 MG MG B 101 1555 1555 2.12 LINK O HOH A 316 MG MG B 101 1555 1555 1.99 LINK O2B APC B 1 MG MG B 101 1555 1555 2.02 LINK MG MG B 101 O HOH B 201 1555 1555 2.04 LINK MG MG B 101 O HOH B 202 1555 1555 2.03 SITE 1 AC1 8 GLU A 54 GLU A 58 GLU A 121 MG A 202 SITE 2 AC1 8 HOH A 308 APC B 1 MG B 101 HOH B 201 SITE 1 AC2 6 GLN A 38 GLU A 58 GLU A 121 MG A 201 SITE 2 AC2 6 HOH A 310 APC B 1 SITE 1 AC3 3 ASN A 18 ARG A 19 GLN A 20 SITE 1 AC4 4 ALA A 47 GLU A 48 LYS A 99 HOH A 398 SITE 1 AC5 7 GLU A 54 MG A 201 HOH A 314 HOH A 316 SITE 2 AC5 7 APC B 1 HOH B 201 HOH B 202 CRYST1 79.631 36.484 58.073 90.00 102.30 90.00 C 1 2 1 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 0.012558 0.000000 0.002737 0.00000 SCALE2 0.000000 0.027409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017624 0.00000